The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges
Identifieur interne : 002586 ( Istex/Corpus ); précédent : 002585; suivant : 002587The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges
Auteurs : E. Ennifar ; M. Yusupov ; P. Walter ; R. Marquet ; B. Ehresmann ; C. Ehresmann ; P. DumasSource :
- Structure [ 0969-2126 ] ; 1999.
English descriptors
- KwdEn :
- Teeft :
- Acta, Acta crystallogr, Adenine, Adenine base, Adenine bulges, Alternate conformations, Alternate positions, Base grip, Base pair, Base pairs, Bifurcated hydrogen bond, Biol, Bulge, Cation, Cationic antibiotics, Cell parameters, Chimeric duplex, Conformation, Crystal forms, Crystal structure, Crystal structures, Crystallization, Crystallization process, Crystallogr, Data collection, Data collection summary, Deep groove, Dimer, Dimerization, Dimerization initiation site, Duplex, Duplex form, Duplex structure, Ehresmann, Endo conformation, Ennifar, Extrahelical, Extrahelical bulges, Extrahelical conformation, First hydration shell, Fourier difference, Fourier difference maps, Genomic, Groove, Hairpin, Hammerhead ribozyme, Helix, Human immunodeficiency virus type, Hydrogen bonds, Important question, Kinked base pair, Local symmetry violation, Lower concentrations, Magnesium, Magnesium atoms, Magnesium binding, Magnesium cations, Magnesium ions, Magnesium signature, Magnesium sites, Manganese, Manganese sites, Maturation step, Methods enzymol, Methods section, Molecular replacement, Moloney murine leukemia virus, Monoclinic, Monoclinic form, Multiple isomorphous replacement, Multiple observations, Natl acad, Next base pair, Noncrystallographic symmetry, Nucleic, Nucleic acids, Nucleocapsid protein, Other cases, Outermost shell, Planar base pair, Positive peaks, Previous results, Redundancy number, Refinement process, Reflections rsym, Research article dimerization site, Reservoir solution, Resolution range, Room temperature, Secondary structure, Solution structure, Space groups, Stable dimer, Statistical analysis, Structural information, Structure solution, Transition state, Trigonal, Trigonal form, Trigonal structure, Twofold axis, Virol, Water molecules.
Abstract
Abstract: Background: An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the formation of a transient ‘kissing-loop complex’ that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far. Results: The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 Å resolution in two different space groups. It reveals a 22 base pair extended duplex with two noncanonical Watson–Crick-like G–A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G–A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the 3′ phosphate of each bulge across an extremely narrowed deep major groove. Conclusions: These crystal structures represent the putative matured form of the initial kissing-loop complex. They show the ability of this self-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking ‘base grip’ that could be a recognition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.
Url:
DOI: 10.1016/S0969-2126(00)80033-7
Links to Exploration step
ISTEX:8ADDDDEEB5354C735EB0B8C66632BCC1D7056659Le document en format XML
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Yusupov</name><affiliation><mods:affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France , Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA</mods:affiliation></affiliation></author><author><name sortKey="Walter, P" sort="Walter, P" uniqKey="Walter P" first="P" last="Walter">P. Walter</name><affiliation><mods:affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</mods:affiliation></affiliation></author><author><name sortKey="Marquet, R" sort="Marquet, R" uniqKey="Marquet R" first="R" last="Marquet">R. Marquet</name><affiliation><mods:affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</mods:affiliation></affiliation></author><author><name sortKey="Ehresmann, B" sort="Ehresmann, B" uniqKey="Ehresmann B" first="B" last="Ehresmann">B. Ehresmann</name><affiliation><mods:affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</mods:affiliation></affiliation></author><author><name sortKey="Ehresmann, C" sort="Ehresmann, C" uniqKey="Ehresmann C" first="C" last="Ehresmann">C. Ehresmann</name><affiliation><mods:affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</mods:affiliation></affiliation></author><author><name sortKey="Dumas, P" sort="Dumas, P" uniqKey="Dumas P" first="P" last="Dumas">P. Dumas</name><affiliation><mods:affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France e-mail: dumas@ibmc.u-strasbg.fr</mods:affiliation></affiliation><affiliation><mods:affiliation>Corresponding author.</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:8ADDDDEEB5354C735EB0B8C66632BCC1D7056659</idno><date when="1999" year="1999">1999</date><idno type="doi">10.1016/S0969-2126(00)80033-7</idno><idno type="url">https://api.istex.fr/ark:/67375/6H6-KTKZ2JJP-T/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">002586</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">002586</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges</title><author><name sortKey="Ennifar, E" sort="Ennifar, E" uniqKey="Ennifar E" first="E" last="Ennifar">E. Ennifar</name><affiliation><mods:affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</mods:affiliation></affiliation></author><author><name sortKey="Yusupov, M" sort="Yusupov, M" uniqKey="Yusupov M" first="M" last="Yusupov">M. Yusupov</name><affiliation><mods:affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France , Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA</mods:affiliation></affiliation></author><author><name sortKey="Walter, P" sort="Walter, P" uniqKey="Walter P" first="P" last="Walter">P. Walter</name><affiliation><mods:affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</mods:affiliation></affiliation></author><author><name sortKey="Marquet, R" sort="Marquet, R" uniqKey="Marquet R" first="R" last="Marquet">R. Marquet</name><affiliation><mods:affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</mods:affiliation></affiliation></author><author><name sortKey="Ehresmann, B" sort="Ehresmann, B" uniqKey="Ehresmann B" first="B" last="Ehresmann">B. Ehresmann</name><affiliation><mods:affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</mods:affiliation></affiliation></author><author><name sortKey="Ehresmann, C" sort="Ehresmann, C" uniqKey="Ehresmann C" first="C" last="Ehresmann">C. Ehresmann</name><affiliation><mods:affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</mods:affiliation></affiliation></author><author><name sortKey="Dumas, P" sort="Dumas, P" uniqKey="Dumas P" first="P" last="Dumas">P. Dumas</name><affiliation><mods:affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France e-mail: dumas@ibmc.u-strasbg.fr</mods:affiliation></affiliation><affiliation><mods:affiliation>Corresponding author.</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Structure</title><title level="j" type="abbrev">STFODE</title><idno type="ISSN">0969-2126</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="1999">1999</date><biblScope unit="volume">7</biblScope><biblScope unit="issue">11</biblScope><biblScope unit="page" from="1439">1439</biblScope><biblScope unit="page" to="1449">1449</biblScope></imprint><idno type="ISSN">0969-2126</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0969-2126</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>HIV-1</term><term>RNA</term><term>X-ray</term><term>bulges</term><term>magnesium</term></keywords><keywords scheme="Teeft" xml:lang="en"><term>Acta</term><term>Acta crystallogr</term><term>Adenine</term><term>Adenine base</term><term>Adenine bulges</term><term>Alternate conformations</term><term>Alternate positions</term><term>Base grip</term><term>Base pair</term><term>Base pairs</term><term>Bifurcated hydrogen bond</term><term>Biol</term><term>Bulge</term><term>Cation</term><term>Cationic antibiotics</term><term>Cell parameters</term><term>Chimeric duplex</term><term>Conformation</term><term>Crystal forms</term><term>Crystal structure</term><term>Crystal structures</term><term>Crystallization</term><term>Crystallization process</term><term>Crystallogr</term><term>Data collection</term><term>Data collection summary</term><term>Deep groove</term><term>Dimer</term><term>Dimerization</term><term>Dimerization initiation site</term><term>Duplex</term><term>Duplex form</term><term>Duplex structure</term><term>Ehresmann</term><term>Endo conformation</term><term>Ennifar</term><term>Extrahelical</term><term>Extrahelical bulges</term><term>Extrahelical conformation</term><term>First hydration shell</term><term>Fourier difference</term><term>Fourier difference maps</term><term>Genomic</term><term>Groove</term><term>Hairpin</term><term>Hammerhead ribozyme</term><term>Helix</term><term>Human immunodeficiency virus type</term><term>Hydrogen bonds</term><term>Important question</term><term>Kinked base pair</term><term>Local symmetry violation</term><term>Lower concentrations</term><term>Magnesium</term><term>Magnesium atoms</term><term>Magnesium binding</term><term>Magnesium cations</term><term>Magnesium ions</term><term>Magnesium signature</term><term>Magnesium sites</term><term>Manganese</term><term>Manganese sites</term><term>Maturation step</term><term>Methods enzymol</term><term>Methods section</term><term>Molecular replacement</term><term>Moloney murine leukemia virus</term><term>Monoclinic</term><term>Monoclinic form</term><term>Multiple isomorphous replacement</term><term>Multiple observations</term><term>Natl acad</term><term>Next base pair</term><term>Noncrystallographic symmetry</term><term>Nucleic</term><term>Nucleic acids</term><term>Nucleocapsid protein</term><term>Other cases</term><term>Outermost shell</term><term>Planar base pair</term><term>Positive peaks</term><term>Previous results</term><term>Redundancy number</term><term>Refinement process</term><term>Reflections rsym</term><term>Research article dimerization site</term><term>Reservoir solution</term><term>Resolution range</term><term>Room temperature</term><term>Secondary structure</term><term>Solution structure</term><term>Space groups</term><term>Stable dimer</term><term>Statistical analysis</term><term>Structural information</term><term>Structure solution</term><term>Transition state</term><term>Trigonal</term><term>Trigonal form</term><term>Trigonal structure</term><term>Twofold axis</term><term>Virol</term><term>Water molecules</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: Background: An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the formation of a transient ‘kissing-loop complex’ that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far. Results: The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 Å resolution in two different space groups. It reveals a 22 base pair extended duplex with two noncanonical Watson–Crick-like G–A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G–A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the 3′ phosphate of each bulge across an extremely narrowed deep major groove. Conclusions: These crystal structures represent the putative matured form of the initial kissing-loop complex. They show the ability of this self-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking ‘base grip’ that could be a recognition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.</div></front></TEI><istex><corpusName>elsevier</corpusName><keywords><teeft><json:string>magnesium</json:string><json:string>dimerization</json:string><json:string>trigonal form</json:string><json:string>duplex</json:string><json:string>ehresmann</json:string><json:string>crystal structure</json:string><json:string>adenine</json:string><json:string>biol</json:string><json:string>helix</json:string><json:string>deep groove</json:string><json:string>dimer</json:string><json:string>genomic</json:string><json:string>monoclinic form</json:string><json:string>acta crystallogr</json:string><json:string>crystallogr</json:string><json:string>acta</json:string><json:string>cation</json:string><json:string>extrahelical</json:string><json:string>virol</json:string><json:string>conformation</json:string><json:string>secondary 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range</json:string><json:string>molecular replacement</json:string><json:string>kinked base pair</json:string><json:string>natl acad</json:string><json:string>space groups</json:string><json:string>transition state</json:string><json:string>stable dimer</json:string><json:string>previous results</json:string><json:string>crystal forms</json:string><json:string>extrahelical conformation</json:string><json:string>solution structure</json:string><json:string>hammerhead ribozyme</json:string><json:string>cationic antibiotics</json:string><json:string>bifurcated hydrogen bond</json:string><json:string>crystallization</json:string></teeft></keywords><author><json:item><name>E Ennifar</name><affiliations><json:string>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</json:string></affiliations></json:item><json:item><name>M Yusupov</name><affiliations><json:string>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France , Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA</json:string></affiliations></json:item><json:item><name>P Walter</name><affiliations><json:string>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</json:string></affiliations></json:item><json:item><name>R Marquet</name><affiliations><json:string>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</json:string></affiliations></json:item><json:item><name>B Ehresmann</name><affiliations><json:string>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</json:string></affiliations></json:item><json:item><name>C Ehresmann</name><affiliations><json:string>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</json:string></affiliations></json:item><json:item><name>P Dumas</name><affiliations><json:string>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France e-mail: dumas@ibmc.u-strasbg.fr</json:string><json:string>Corresponding author.</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>Research Paper</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>bulges</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>HIV-1</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>magnesium</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>RNA</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>X-ray</value></json:item></subject><arkIstex>ark:/67375/6H6-KTKZ2JJP-T</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>Full-length article</json:string></originalGenre><abstract>Abstract: Background: An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the formation of a transient ‘kissing-loop complex’ that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far. Results: The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 Å resolution in two different space groups. It reveals a 22 base pair extended duplex with two noncanonical Watson–Crick-like G–A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G–A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the 3′ phosphate of each bulge across an extremely narrowed deep major groove. Conclusions: These crystal structures represent the putative matured form of the initial kissing-loop complex. They show the ability of this self-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking ‘base grip’ that could be a recognition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.</abstract><qualityIndicators><score>9.82</score><pdfWordCount>7189</pdfWordCount><pdfCharCount>43406</pdfCharCount><pdfVersion>1.3</pdfVersion><pdfPageCount>11</pdfPageCount><pdfPageSize>595 x 842 pts (A4)</pdfPageSize><refBibsNative>true</refBibsNative><abstractWordCount>235</abstractWordCount><abstractCharCount>1603</abstractCharCount><keywordCount>6</keywordCount></qualityIndicators><title>The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges</title><pmid><json:string>10574792</json:string></pmid><pii><json:string>S0969-2126(00)80033-7</json:string></pii><genre><json:string>research-article</json:string></genre><host><title>Structure</title><language><json:string>unknown</json:string></language><publicationDate>1999</publicationDate><issn><json:string>0969-2126</json:string></issn><pii><json:string>S0969-2126(00)X0097-4</json:string></pii><volume>7</volume><issue>11</issue><pages><first>1439</first><last>1449</last></pages><genre><json:string>journal</json:string></genre></host><namedEntities><unitex><date><json:string>1999</json:string><json:string>1446</json:string></date><geogName></geogName><orgName><json:string>Sinsheimer Laboratories</json:string><json:string>Research Article Dimerization</json:string><json:string>University of California, Santa Cruz</json:string><json:string>and Research Article Dimerization</json:string><json:string>Elsevier Science Ltd.</json:string><json:string>Agence Nationale</json:string></orgName><orgName_funder><json:string>Agence Nationale</json:string></orgName_funder><orgName_provider></orgName_provider><persName><json:string>Stereoviews</json:string></persName><placeName><json:string>Grenoble</json:string><json:string>France</json:string><json:string>Cambridge</json:string></placeName><ref_url></ref_url><ref_bibl><json:string>[50]</json:string><json:string>[4]</json:string><json:string>[10,11]</json:string><json:string>[7,8]</json:string><json:string>[56]</json:string><json:string>[18]</json:string><json:string>Mujeeb et al. [8]</json:string><json:string>[55]</json:string><json:string>[8]</json:string><json:string>[17]</json:string><json:string>[47,48]</json:string><json:string>[17,45,46]</json:string><json:string>[11,35]</json:string><json:string>[49]</json:string><json:string>[3]</json:string><json:string>[53]</json:string><json:string>Ennifar et al. 1447</json:string><json:string>[5]</json:string><json:string>[34,35]</json:string><json:string>[6,7]</json:string><json:string>[52]</json:string><json:string>[9]</json:string><json:string>[1,2]</json:string><json:string>[51]</json:string><json:string>[3,5,6]</json:string><json:string>[24]</json:string><json:string>Ennifar et al. 1445</json:string><json:string>[19]</json:string></ref_bibl><bibl></bibl></unitex></namedEntities><ark><json:string>ark:/67375/6H6-KTKZ2JJP-T</json:string></ark><categories><wos><json:string>1 - science</json:string><json:string>2 - cell biology</json:string><json:string>2 - biophysics</json:string><json:string>2 - biochemistry & molecular biology</json:string></wos><scienceMetrix><json:string>1 - health sciences</json:string><json:string>2 - biomedical research</json:string><json:string>3 - biophysics</json:string></scienceMetrix><scopus><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Molecular Biology</json:string><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Structural Biology</json:string></scopus><inist><json:string>1 - sciences appliquees, technologies et medecines</json:string><json:string>2 - sciences biologiques et medicales</json:string><json:string>3 - sciences biologiques fondamentales et appliquees. psychologie</json:string><json:string>4 - microbiologie</json:string></inist></categories><publicationDate>1999</publicationDate><copyrightDate>1999</copyrightDate><doi><json:string>10.1016/S0969-2126(00)80033-7</json:string></doi><id>8ADDDDEEB5354C735EB0B8C66632BCC1D7056659</id><score>1</score><fulltext><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-KTKZ2JJP-T/fulltext.pdf</uri></json:item><json:item><extension>zip</extension><original>false</original><mimetype>application/zip</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-KTKZ2JJP-T/bundle.zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/ark:/67375/6H6-KTKZ2JJP-T/fulltext.tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main" xml:lang="en">The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher scheme="https://scientific-publisher.data.istex.fr">ELSEVIER</publisher><availability><licence><p>©1999 Elsevier Science Ltd</p></licence><p scheme="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-HKKZVM7B-M">elsevier</p></availability><date>1999</date></publicationStmt><notesStmt><note type="research-article" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</note><note type="journal" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note><note type="content">Section title: Research Article</note><note type="content">Figure 1: Localization, and primary and secondary structure of the DIS. (a) Secondary structure and localization of the four stem-loops SL1, SL2, SL3 and SL4 forming the encapsidation site. The fragment of SL1 that has been crystallized is boxed. SD stands for splice donor site. The initiation codon of gag is highlighted by an arrow. (b) Secondary structure of two DISs of 23 nucleotides forming a kissing-loop complex. (c) Expected secondary structure of the extended duplex form. (d) Secondary structure of the extended duplex as seen in the crystal. The bulged-out adenine base, numbered 8 in this structure, corresponds to A272 in the full-length viral RNA.</note><note type="content">Figure 2: General views of the DIS structure (trigonal form). (a) Stereoview of the DIS structure. The angle between the upper and lower parts of the helical axis is about 13°. Strands labelled a and b are coloured red and green, respectively. Magnesium ions are shown as yellow spheres and are labelled with Greek letters. The residue A8b is shown with its two alternate conformations (see text). The noncrystallographic axis of symmetry is coincident with the line passing through Mg δ and Mg ϵ. (b,c) Solvent-accessible surface of the structure with the negative charges in red and the positively charged magnesium represented by blue spheres. Bulged residues A8a and A8b (in its C2′ endo conformation) are in pastel green. The picture emphasizes the deep-groove widening as a result of the planar G–A base pair and the ‘magnesium-clamp’ motif with an extremely narrowed deep groove (c).</note><note type="content">Figure 3: Close-up views of the Watson–Crick-like G–A mismatches (trigonal form). (a) View of the G9a–A16b base pair emphasizing the bifurcated hydrogen bond between G9a(N2) and C17b(O2) that results from large buckle and propeller-twist angles. (b) View of the almost planar G9B–A16a base pair which, at variance with the kinked G9a–A16a base pair, induces a local broadening of the deep groove by about 2.5 Å. For the sake of clarity, A8b is represented here in only one (C3′ endo) of the two alternate conformations.</note><note type="content">Figure 4: Interactions of the bulged residues. (a) Interaction between the bases of the bulged A8a and of G4b of a symmetry-related molecule (G4b′ on the figure) in the trigonal form. Note the existence of an unusual C–H–N bond. Hydrogen-bond lengths are drawn and labelled in green. (b) Stereoview of the base-stacking interaction in the trigonal form between A8b (C2′ endo; green) and A8b′ (C3′ endo; purple) resulting from local symmetry violation around a twofold axis (the base of A8b lies on the symmetry axis). (c) Stereoview of A8b (green) in the monoclinic form, interacting with residues C5a (light green) and C20b (magenta) of a symmetry-related molecule. The 2.8 Å resolution (3Fobs–2Fcalc) electron-density map, contoured at 1.4σ, also shows the partially dehydrated magnesium γ (yellow sphere). Five hydrogen bonds (dotted lines) stabilize the bulged residue.</note><note type="content">Figure 5: Stereoview of the (2Fobs–Fcalc) electron-density map (light blue) around the hexahydrated magnesium site β′, showing the first hydration shell of this cation and three water molecules of its second hydration shell. The (FMnobs–FMgcalc) Fourier difference map contoured at 4σ is superimposed in orange.</note><note type="content">Figure 6: Stereoviews showing the closing of the deep groove in the vicinity of the bulges and three magnesium cations with direct coordination to phosphates and N7 atoms (trigonal form). (a) Axial coordination of Mg δ by the phosphates of G9a and G9b. Mg γ and γ′ are each localized in a pocket formed by the phosphate of A8 and the N7 of G9 of strands b and a, respectively. The ribose of A8a adopts the C3′ endo/O4′ endo conformation and its base is in the syn conformation, whereas the ribose of A8b is shown here in one of the two conformations (C2′ endo). The line of sight is along the noncrystallographic dyad axis. (b) Representative (2Fobs–Fcalc) electron-density map (light blue), superimposed with the (FMnobs–FMgcalc) Fourier difference map (orange), contoured at 4σ around site δ and at 6σ around sites γ and γ′ (see the Materials and methods section).</note><note type="content">Table 1: Distances of magnesium atoms from closest water or RNA atoms (trigonal form).</note><note type="content">Table 2: Data collection summary and phasing statistics for the trigonal form.</note><note type="content">Table 3: Data collection summary for the monoclinic form.</note><note type="content">Table 4: Refinement statistics∗.</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges</title><author xml:id="author-0000"><persName><forename type="first">E</forename><surname>Ennifar</surname></persName><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</affiliation></author><author xml:id="author-0001"><persName><forename type="first">M</forename><surname>Yusupov</surname></persName><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France , Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA</affiliation></author><author xml:id="author-0002"><persName><forename type="first">P</forename><surname>Walter</surname></persName><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</affiliation></author><author xml:id="author-0003"><persName><forename type="first">R</forename><surname>Marquet</surname></persName><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</affiliation></author><author xml:id="author-0004"><persName><forename type="first">B</forename><surname>Ehresmann</surname></persName><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</affiliation></author><author xml:id="author-0005"><persName><forename type="first">C</forename><surname>Ehresmann</surname></persName><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</affiliation></author><author xml:id="author-0006"><persName><forename type="first">P</forename><surname>Dumas</surname></persName><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France e-mail: dumas@ibmc.u-strasbg.fr</affiliation><affiliation>Corresponding author.</affiliation></author><idno type="istex">8ADDDDEEB5354C735EB0B8C66632BCC1D7056659</idno><idno type="ark">ark:/67375/6H6-KTKZ2JJP-T</idno><idno type="DOI">10.1016/S0969-2126(00)80033-7</idno><idno type="PII">S0969-2126(00)80033-7</idno></analytic><monogr><title level="j">Structure</title><title level="j" type="abbrev">STFODE</title><idno type="pISSN">0969-2126</idno><idno type="PII">S0969-2126(00)X0097-4</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="1999"></date><biblScope unit="volume">7</biblScope><biblScope unit="issue">11</biblScope><biblScope unit="page" from="1439">1439</biblScope><biblScope unit="page" to="1449">1449</biblScope></imprint></monogr></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>1999</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>Abstract: Background: An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the formation of a transient ‘kissing-loop complex’ that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far. Results: The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 Å resolution in two different space groups. It reveals a 22 base pair extended duplex with two noncanonical Watson–Crick-like G–A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G–A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the 3′ phosphate of each bulge across an extremely narrowed deep major groove. Conclusions: These crystal structures represent the putative matured form of the initial kissing-loop complex. They show the ability of this self-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking ‘base grip’ that could be a recognition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.</p></abstract><textClass><keywords scheme="keyword"><list><head>article-category</head><item><term>Research Paper</term></item></list></keywords></textClass><textClass xml:lang="en"><keywords scheme="keyword"><list><head>Keywords</head><item><term>bulges</term></item><item><term>HIV-1</term></item><item><term>magnesium</term></item><item><term>RNA</term></item><item><term>X-ray</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="1999-07-29">Modified</change><change when="1999">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-KTKZ2JJP-T/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Elsevier, elements deleted: ce:floats; body; tail"><istex:xmlDeclaration>version="1.0" encoding="utf-8"</istex:xmlDeclaration><istex:docType PUBLIC="-//ES//DTD journal article DTD version 4.5.2//EN//XML" URI="art452.dtd" name="istex:docType"><istex:entity SYSTEM="gr1" NDATA="IMAGE" name="gr1"></istex:entity><istex:entity SYSTEM="gr2" NDATA="IMAGE" name="gr2"></istex:entity><istex:entity SYSTEM="gr3" NDATA="IMAGE" name="gr3"></istex:entity><istex:entity SYSTEM="gr4" NDATA="IMAGE" name="gr4"></istex:entity><istex:entity SYSTEM="gr5" NDATA="IMAGE" name="gr5"></istex:entity><istex:entity SYSTEM="gr6" NDATA="IMAGE" name="gr6"></istex:entity></istex:docType><istex:document><converted-article version="4.5.2" docsubtype="fla" xml:lang="en"><item-info><jid>STFODE</jid><aid>17</aid><ce:pii>S0969-2126(00)80033-7</ce:pii><ce:doi>10.1016/S0969-2126(00)80033-7</ce:doi><ce:copyright type="full-transfer" year="1999">Elsevier Science Ltd</ce:copyright><ce:doctopics><ce:doctopic><ce:text>Research Paper</ce:text></ce:doctopic></ce:doctopics></item-info><head><ce:dochead><ce:textfn>Research Article</ce:textfn></ce:dochead><ce:title>The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges</ce:title><ce:author-group><ce:author biographyid="BIO1"><ce:given-name>E</ce:given-name><ce:surname>Ennifar</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>1</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>M</ce:given-name><ce:surname>Yusupov</ce:surname><ce:cross-ref refid="AFF2"><ce:sup>2</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>P</ce:given-name><ce:surname>Walter</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>1</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>R</ce:given-name><ce:surname>Marquet</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>1</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>B</ce:given-name><ce:surname>Ehresmann</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>1</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>C</ce:given-name><ce:surname>Ehresmann</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>1</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>P</ce:given-name><ce:surname>Dumas</ce:surname><ce:cross-ref refid="AFF3"><ce:sup>3</ce:sup></ce:cross-ref><ce:cross-ref refid="COR1">*</ce:cross-ref></ce:author><ce:affiliation id="AFF1"><ce:label>1</ce:label><ce:textfn>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</ce:textfn></ce:affiliation><ce:affiliation id="AFF2"><ce:label>2</ce:label><ce:textfn>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France , Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA</ce:textfn></ce:affiliation><ce:affiliation id="AFF3"><ce:label>3</ce:label><ce:textfn>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France e-mail: <ce:inter-ref xlink:href="mailto:dumas@ibmc.u-strasbg.fr">dumas@ibmc.u-strasbg.fr</ce:inter-ref></ce:textfn></ce:affiliation><ce:correspondence id="COR1"><ce:label>*</ce:label><ce:text>Corresponding author.</ce:text></ce:correspondence></ce:author-group><ce:date-received day="8" month="6" year="1999"></ce:date-received><ce:date-revised day="29" month="7" year="1999"></ce:date-revised><ce:date-accepted day="9" month="8" year="1999"></ce:date-accepted><ce:abstract><ce:section-title>Abstract</ce:section-title><ce:abstract-sec><ce:simple-para><ce:bold>Background:</ce:bold> An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the formation of a transient ‘kissing-loop complex’ that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far.</ce:simple-para><ce:simple-para><ce:bold>Results:</ce:bold> The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 Å resolution in two different space groups. It reveals a 22 base pair extended duplex with two noncanonical Watson–Crick-like G–A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G–A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the 3′ phosphate of each bulge across an extremely narrowed deep major groove.</ce:simple-para><ce:simple-para><ce:bold>Conclusions:</ce:bold> These crystal structures represent the putative matured form of the initial kissing-loop complex. They show the ability of this self-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking ‘base grip’ that could be a recognition signal, either in <ce:italic>cis</ce:italic> for another viral RNA sequence, or in <ce:italic>trans</ce:italic> for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.</ce:simple-para></ce:abstract-sec></ce:abstract><ce:keywords class="keyword"><ce:section-title>Keywords</ce:section-title><ce:keyword><ce:text>bulges</ce:text></ce:keyword><ce:keyword><ce:text>HIV-1</ce:text></ce:keyword><ce:keyword><ce:text>magnesium</ce:text></ce:keyword><ce:keyword><ce:text>RNA</ce:text></ce:keyword><ce:keyword><ce:text>X-ray</ce:text></ce:keyword></ce:keywords></head></converted-article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges</title></titleInfo><titleInfo type="alternative" lang="en" contentType="CDATA"><title>The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges</title></titleInfo><name type="personal"><namePart type="given">E</namePart><namePart type="family">Ennifar</namePart><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">M</namePart><namePart type="family">Yusupov</namePart><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France , Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">P</namePart><namePart type="family">Walter</namePart><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">R</namePart><namePart type="family">Marquet</namePart><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">B</namePart><namePart type="family">Ehresmann</namePart><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">C</namePart><namePart type="family">Ehresmann</namePart><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">P</namePart><namePart type="family">Dumas</namePart><affiliation>UPR9002 – Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, F-67084, Strasbourg cedex, France e-mail: dumas@ibmc.u-strasbg.fr</affiliation><affiliation>Corresponding author.</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="Full-length article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">1999</dateIssued><dateModified encoding="w3cdtf">1999-07-29</dateModified><copyrightDate encoding="w3cdtf">1999</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><abstract lang="en">Abstract: Background: An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the formation of a transient ‘kissing-loop complex’ that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far. Results: The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 Å resolution in two different space groups. It reveals a 22 base pair extended duplex with two noncanonical Watson–Crick-like G–A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G–A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the 3′ phosphate of each bulge across an extremely narrowed deep major groove. Conclusions: These crystal structures represent the putative matured form of the initial kissing-loop complex. They show the ability of this self-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking ‘base grip’ that could be a recognition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.</abstract><note type="content">Section title: Research Article</note><note type="content">Figure 1: Localization, and primary and secondary structure of the DIS. (a) Secondary structure and localization of the four stem-loops SL1, SL2, SL3 and SL4 forming the encapsidation site. The fragment of SL1 that has been crystallized is boxed. SD stands for splice donor site. The initiation codon of gag is highlighted by an arrow. (b) Secondary structure of two DISs of 23 nucleotides forming a kissing-loop complex. (c) Expected secondary structure of the extended duplex form. (d) Secondary structure of the extended duplex as seen in the crystal. The bulged-out adenine base, numbered 8 in this structure, corresponds to A272 in the full-length viral RNA.</note><note type="content">Figure 2: General views of the DIS structure (trigonal form). (a) Stereoview of the DIS structure. The angle between the upper and lower parts of the helical axis is about 13°. Strands labelled a and b are coloured red and green, respectively. Magnesium ions are shown as yellow spheres and are labelled with Greek letters. The residue A8b is shown with its two alternate conformations (see text). The noncrystallographic axis of symmetry is coincident with the line passing through Mg δ and Mg ϵ. (b,c) Solvent-accessible surface of the structure with the negative charges in red and the positively charged magnesium represented by blue spheres. Bulged residues A8a and A8b (in its C2′ endo conformation) are in pastel green. The picture emphasizes the deep-groove widening as a result of the planar G–A base pair and the ‘magnesium-clamp’ motif with an extremely narrowed deep groove (c).</note><note type="content">Figure 3: Close-up views of the Watson–Crick-like G–A mismatches (trigonal form). (a) View of the G9a–A16b base pair emphasizing the bifurcated hydrogen bond between G9a(N2) and C17b(O2) that results from large buckle and propeller-twist angles. (b) View of the almost planar G9B–A16a base pair which, at variance with the kinked G9a–A16a base pair, induces a local broadening of the deep groove by about 2.5 Å. For the sake of clarity, A8b is represented here in only one (C3′ endo) of the two alternate conformations.</note><note type="content">Figure 4: Interactions of the bulged residues. (a) Interaction between the bases of the bulged A8a and of G4b of a symmetry-related molecule (G4b′ on the figure) in the trigonal form. Note the existence of an unusual C–H–N bond. Hydrogen-bond lengths are drawn and labelled in green. (b) Stereoview of the base-stacking interaction in the trigonal form between A8b (C2′ endo; green) and A8b′ (C3′ endo; purple) resulting from local symmetry violation around a twofold axis (the base of A8b lies on the symmetry axis). (c) Stereoview of A8b (green) in the monoclinic form, interacting with residues C5a (light green) and C20b (magenta) of a symmetry-related molecule. The 2.8 Å resolution (3Fobs–2Fcalc) electron-density map, contoured at 1.4σ, also shows the partially dehydrated magnesium γ (yellow sphere). Five hydrogen bonds (dotted lines) stabilize the bulged residue.</note><note type="content">Figure 5: Stereoview of the (2Fobs–Fcalc) electron-density map (light blue) around the hexahydrated magnesium site β′, showing the first hydration shell of this cation and three water molecules of its second hydration shell. The (FMnobs–FMgcalc) Fourier difference map contoured at 4σ is superimposed in orange.</note><note type="content">Figure 6: Stereoviews showing the closing of the deep groove in the vicinity of the bulges and three magnesium cations with direct coordination to phosphates and N7 atoms (trigonal form). (a) Axial coordination of Mg δ by the phosphates of G9a and G9b. Mg γ and γ′ are each localized in a pocket formed by the phosphate of A8 and the N7 of G9 of strands b and a, respectively. The ribose of A8a adopts the C3′ endo/O4′ endo conformation and its base is in the syn conformation, whereas the ribose of A8b is shown here in one of the two conformations (C2′ endo). The line of sight is along the noncrystallographic dyad axis. (b) Representative (2Fobs–Fcalc) electron-density map (light blue), superimposed with the (FMnobs–FMgcalc) Fourier difference map (orange), contoured at 4σ around site δ and at 6σ around sites γ and γ′ (see the Materials and methods section).</note><note type="content">Table 1: Distances of magnesium atoms from closest water or RNA atoms (trigonal form).</note><note type="content">Table 2: Data collection summary and phasing statistics for the trigonal form.</note><note type="content">Table 3: Data collection summary for the monoclinic form.</note><note type="content">Table 4: Refinement statistics∗.</note><subject><genre>article-category</genre><topic>Research Paper</topic></subject><subject lang="en"><genre>Keywords</genre><topic>bulges</topic><topic>HIV-1</topic><topic>magnesium</topic><topic>RNA</topic><topic>X-ray</topic></subject><relatedItem type="host"><titleInfo><title>Structure</title></titleInfo><titleInfo type="abbreviated"><title>STFODE</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">1999</dateIssued></originInfo><identifier type="ISSN">0969-2126</identifier><identifier type="PII">S0969-2126(00)X0097-4</identifier><part><date>1999</date><detail type="volume"><number>7</number><caption>vol.</caption></detail><detail type="issue"><number>11</number><caption>no.</caption></detail><extent unit="issue-pages"><start>R251</start><end>R274</end></extent><extent unit="issue-pages"><start>1311</start><end>1449</end></extent><extent unit="pages"><start>1439</start><end>1449</end></extent></part></relatedItem><identifier type="istex">8ADDDDEEB5354C735EB0B8C66632BCC1D7056659</identifier><identifier type="ark">ark:/67375/6H6-KTKZ2JJP-T</identifier><identifier type="DOI">10.1016/S0969-2126(00)80033-7</identifier><identifier type="PII">S0969-2126(00)80033-7</identifier><accessCondition type="use and reproduction" contentType="copyright">©1999 Elsevier Science Ltd</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-HKKZVM7B-M">elsevier</recordContentSource><recordOrigin>Elsevier Science Ltd, ©1999</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-KTKZ2JJP-T/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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