The crystal structure of bacteriophage GA and a comparison of bacteriophages belonging to the major groups of Escherichia coli leviviruses
Identifieur interne : 002670 ( Istex/Corpus ); précédent : 002669; suivant : 002671The crystal structure of bacteriophage GA and a comparison of bacteriophages belonging to the major groups of Escherichia coli leviviruses
Auteurs : Kaspars Tars ; Maija Bundule ; Kerstin Fridborg ; Lars LiljasSource :
- Journal of Molecular Biology [ 0022-2836 ] ; 1997.
English descriptors
- KwdEn :
- GA, MS2, Qβ, virus assembly, virus evolution.
- Teeft :
- Academic press, Acid residues, Adenine bases, Amino, Amino acid residues, Amino acid sequence, Ammonium sulphate, Arginine residues, Assembly intermediates, Assembly pathway, Bacteriophage, Binding site, Binding sites, Biol, Capsid, Capsid formation, Capsid structure, Coat protein, Coat protein dimer, Coat protein gene, Coat protein mutants, Coat proteins, Cold spring harbor, Cold spring harbor laboratory press, Coliphage, Conformation, Crystal structure, Data collection, Different conformations, Dimer, Dimer crystal structure, Disulphide bridges, Electron density, Extra residue, Glycine residues, Golmohammadi, Helix, Hohn, Hydrogen bond, Hydrogen bonds, Hydrophobic, Hydrophobic core, Hydrophobic interactions, Icosahedral, Independent subunits, Individual subunits, Inner surface, Interaction, Interdimer interactions, Liljas, Loop conformations, Loop regions, Molecular replacement, Monomer, Mutant, Mutation, Mutation experiments, Outer surface, Particle assembly, Peabody, Pentamers, Phage, Phage particles, Phosphate groups, Plenum publishing corporation, Polar interactions, Proline residue, Protein shells, Replicase gene, Residue, Same orientation, Secondary structure elements, Sequence similarities, Stereo view, Stockley, Stonehouse, Subunit, Terminus, Trans conformation, Uhlenbeck, Valegard, Viral, Virus assembly.
Abstract
Abstract: The three-dimensional structure of the small T = 3 RNA bacteriophage GA has been determined at 3.4 Å resolution. The structure was solved by molecular replacement, using the phage MS2 as an initial model. A comparison of the protein shells of the four related phages GA, MS2, fr and Qβ was carried out in order to define structural features of particular importance for their assembly and specific RNA interaction. A high degree of similarity was found in the RNA binding sites, whereas larger structural differences are located in the loop regions of the coat proteins, especially in the FG loops forming 5-fold and quasi-6-fold contacts. The overall arrangement of the protein subunits in the shells of these phages is very similar, although the details of the interactions differ. The few conserved interactions are suggested to govern the subunit packing during assembly.
Url:
DOI: 10.1006/jmbi.1997.1214
Links to Exploration step
ISTEX:700B1758131F103787DB2DB48B8FBF2612F3DE45Le document en format XML
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of Molecular Biology Uppsala University Box 590, S-751 24 Uppsala, Sweden</mods:affiliation></affiliation></author><author><name sortKey="Liljas, Lars" sort="Liljas, Lars" uniqKey="Liljas L" first="Lars" last="Liljas">Lars Liljas</name><affiliation><mods:affiliation>Department of Molecular Biology Uppsala University Box 590, S-751 24 Uppsala, Sweden</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:700B1758131F103787DB2DB48B8FBF2612F3DE45</idno><date when="1997" year="1997">1997</date><idno type="doi">10.1006/jmbi.1997.1214</idno><idno type="url">https://api.istex.fr/ark:/67375/6H6-2HL7QSCZ-Q/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">002670</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">002670</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">The crystal structure of bacteriophage GA and a comparison of bacteriophages belonging to the major groups of Escherichia coli leviviruses</title><author><name sortKey="Tars, Kaspars" sort="Tars, Kaspars" uniqKey="Tars K" first="Kaspars" last="Tars">Kaspars Tars</name><affiliation><mods:affiliation>Biomedical Research and Study Centre, Latvian University, Ratsupites 1, Riga, Latvia</mods:affiliation></affiliation></author><author><name sortKey="Bundule, Maija" sort="Bundule, Maija" uniqKey="Bundule M" first="Maija" last="Bundule">Maija Bundule</name><affiliation><mods:affiliation>Biomedical Research and Study Centre, Latvian University, Ratsupites 1, Riga, Latvia</mods:affiliation></affiliation></author><author><name sortKey="Fridborg, Kerstin" sort="Fridborg, Kerstin" uniqKey="Fridborg K" first="Kerstin" last="Fridborg">Kerstin Fridborg</name><affiliation><mods:affiliation>Department of Molecular Biology Uppsala University Box 590, S-751 24 Uppsala, Sweden</mods:affiliation></affiliation></author><author><name sortKey="Liljas, Lars" sort="Liljas, Lars" uniqKey="Liljas L" first="Lars" last="Liljas">Lars Liljas</name><affiliation><mods:affiliation>Department of Molecular Biology Uppsala University Box 590, S-751 24 Uppsala, Sweden</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Journal of Molecular Biology</title><title level="j" type="abbrev">YJMBI</title><idno type="ISSN">0022-2836</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="1997">1997</date><biblScope unit="volume">271</biblScope><biblScope unit="issue">5</biblScope><biblScope unit="page" from="759">759</biblScope><biblScope unit="page" to="773">773</biblScope></imprint><idno type="ISSN">0022-2836</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0022-2836</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>GA</term><term>MS2</term><term>Qβ</term><term>virus assembly</term><term>virus evolution</term></keywords><keywords scheme="Teeft" xml:lang="en"><term>Academic press</term><term>Acid residues</term><term>Adenine bases</term><term>Amino</term><term>Amino acid residues</term><term>Amino acid sequence</term><term>Ammonium sulphate</term><term>Arginine residues</term><term>Assembly intermediates</term><term>Assembly pathway</term><term>Bacteriophage</term><term>Binding site</term><term>Binding sites</term><term>Biol</term><term>Capsid</term><term>Capsid formation</term><term>Capsid structure</term><term>Coat protein</term><term>Coat protein dimer</term><term>Coat protein gene</term><term>Coat protein mutants</term><term>Coat proteins</term><term>Cold spring harbor</term><term>Cold spring harbor laboratory press</term><term>Coliphage</term><term>Conformation</term><term>Crystal structure</term><term>Data collection</term><term>Different conformations</term><term>Dimer</term><term>Dimer crystal structure</term><term>Disulphide bridges</term><term>Electron density</term><term>Extra residue</term><term>Glycine residues</term><term>Golmohammadi</term><term>Helix</term><term>Hohn</term><term>Hydrogen bond</term><term>Hydrogen bonds</term><term>Hydrophobic</term><term>Hydrophobic core</term><term>Hydrophobic interactions</term><term>Icosahedral</term><term>Independent subunits</term><term>Individual subunits</term><term>Inner surface</term><term>Interaction</term><term>Interdimer interactions</term><term>Liljas</term><term>Loop conformations</term><term>Loop regions</term><term>Molecular replacement</term><term>Monomer</term><term>Mutant</term><term>Mutation</term><term>Mutation experiments</term><term>Outer surface</term><term>Particle assembly</term><term>Peabody</term><term>Pentamers</term><term>Phage</term><term>Phage particles</term><term>Phosphate groups</term><term>Plenum publishing corporation</term><term>Polar interactions</term><term>Proline residue</term><term>Protein shells</term><term>Replicase gene</term><term>Residue</term><term>Same orientation</term><term>Secondary structure elements</term><term>Sequence similarities</term><term>Stereo view</term><term>Stockley</term><term>Stonehouse</term><term>Subunit</term><term>Terminus</term><term>Trans conformation</term><term>Uhlenbeck</term><term>Valegard</term><term>Viral</term><term>Virus assembly</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: The three-dimensional structure of the small T = 3 RNA bacteriophage GA has been determined at 3.4 Å resolution. The structure was solved by molecular replacement, using the phage MS2 as an initial model. A comparison of the protein shells of the four related phages GA, MS2, fr and Qβ was carried out in order to define structural features of particular importance for their assembly and specific RNA interaction. A high degree of similarity was found in the RNA binding sites, whereas larger structural differences are located in the loop regions of the coat proteins, especially in the FG loops forming 5-fold and quasi-6-fold contacts. The overall arrangement of the protein subunits in the shells of these phages is very similar, although the details of the interactions differ. The few conserved interactions are suggested to govern the subunit packing during assembly.</div></front></TEI><istex><corpusName>elsevier</corpusName><keywords><teeft><json:string>dimer</json:string><json:string>subunit</json:string><json:string>phage</json:string><json:string>bacteriophage</json:string><json:string>capsid</json:string><json:string>crystal structure</json:string><json:string>coat 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sequence</json:string><json:string>independent subunits</json:string><json:string>plenum publishing corporation</json:string><json:string>cold spring harbor laboratory press</json:string><json:string>cold spring harbor</json:string></teeft></keywords><author><json:item><name>Kaspars Tars</name><affiliations><json:string>Biomedical Research and Study Centre, Latvian University, Ratsupites 1, Riga, Latvia</json:string></affiliations></json:item><json:item><name>Maija Bundule</name><affiliations><json:string>Biomedical Research and Study Centre, Latvian University, Ratsupites 1, Riga, Latvia</json:string></affiliations></json:item><json:item><name>Kerstin Fridborg</name><affiliations><json:string>Department of Molecular Biology Uppsala University Box 590, S-751 24 Uppsala, Sweden</json:string></affiliations></json:item><json:item><name>Lars Liljas</name><affiliations><json:string>Department of Molecular Biology Uppsala University Box 590, S-751 24 Uppsala, Sweden</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>Regular article</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>MS2</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>GA</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Qβ</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>virus assembly</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>virus evolution</value></json:item></subject><arkIstex>ark:/67375/6H6-2HL7QSCZ-Q</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>Full-length article</json:string></originalGenre><abstract>Abstract: The three-dimensional structure of the small T = 3 RNA bacteriophage GA has been determined at 3.4 Å resolution. The structure was solved by molecular replacement, using the phage MS2 as an initial model. A comparison of the protein shells of the four related phages GA, MS2, fr and Qβ was carried out in order to define structural features of particular importance for their assembly and specific RNA interaction. A high degree of similarity was found in the RNA binding sites, whereas larger structural differences are located in the loop regions of the coat proteins, especially in the FG loops forming 5-fold and quasi-6-fold contacts. The overall arrangement of the protein subunits in the shells of these phages is very similar, although the details of the interactions differ. The few conserved interactions are suggested to govern the subunit packing during assembly.</abstract><qualityIndicators><score>8.704</score><pdfWordCount>7786</pdfWordCount><pdfCharCount>44277</pdfCharCount><pdfVersion>1.3</pdfVersion><pdfPageCount>15</pdfPageCount><pdfPageSize>595 x 842 pts (A4)</pdfPageSize><refBibsNative>true</refBibsNative><abstractWordCount>142</abstractWordCount><abstractCharCount>885</abstractCharCount><keywordCount>6</keywordCount></qualityIndicators><title>The crystal structure of bacteriophage GA and a comparison of bacteriophages belonging to the major groups of Escherichia coli leviviruses</title><pmid><json:string>9299325</json:string></pmid><pii><json:string>S0022-2836(97)91214-6</json:string></pii><genre><json:string>research-article</json:string></genre><serie><title>Comprehensive Virology</title><language><json:string>unknown</json:string></language><volume>vol. 13</volume><pages><first>69</first><last>204</last></pages><editor><json:item><name>H. Fraenkel-Conrat</name></json:item><json:item><name>R.R Wagner</name></json:item></editor></serie><host><title>Journal of Molecular Biology</title><language><json:string>unknown</json:string></language><publicationDate>1997</publicationDate><issn><json:string>0022-2836</json:string></issn><pii><json:string>S0022-2836(00)X0097-6</json:string></pii><volume>271</volume><issue>5</issue><pages><first>759</first><last>773</last></pages><genre><json:string>journal</json:string></genre></host><namedEntities><unitex><date><json:string>1997</json:string></date><geogName></geogName><orgName><json:string>Department of Molecular Biology, Uppsala University Box</json:string><json:string>Latvian Science Council</json:string><json:string>Royal Swedish Academy of Sciences</json:string><json:string>Swedish Natural Science Research Council</json:string></orgName><orgName_funder><json:string>Latvian Science Council</json:string><json:string>Royal Swedish Academy of Sciences</json:string><json:string>Swedish Natural Science Research Council</json:string></orgName_funder><orgName_provider></orgName_provider><persName><json:string>W. Minor</json:string><json:string>Crystal Structure</json:string><json:string>Z. Otwinowski</json:string><json:string>Table</json:string><json:string>N. Stonehouse</json:string><json:string>Groups</json:string><json:string>S. van den Worm</json:string><json:string>Dr A. Dishler</json:string><json:string>Lars Liljas</json:string><json:string>Diagram</json:string><json:string>An Asp</json:string></persName><placeName><json:string>Uppsala</json:string><json:string>UK</json:string><json:string>Puri</json:string><json:string>Latvia</json:string><json:string>Sweden</json:string></placeName><ref_url></ref_url><ref_bibl><json:string>Simon et al., 1994</json:string><json:string>Carey et al., 1983</json:string><json:string>Jones et al., 1990</json:string><json:string>Dhaese et al., 1979</json:string><json:string>CCP4; Collaborative Computational Project, 1994</json:string><json:string>Hill et al., 1997</json:string><json:string>Caspar & Klug, 1962</json:string><json:string>Golmohammadi et al., 1996</json:string><json:string>Tong & Rossmann, 1990</json:string><json:string>Lim et al., 1994</json:string><json:string>Hung, 1976</json:string><json:string>Eggen & Nathans, 1969</json:string><json:string>Liljas et al., 1994</json:string><json:string>Kleywegt & Jones, 1994</json:string><json:string>Pushko et al., 1993</json:string><json:string>Peabody & Ely, 1992</json:string><json:string>Chothia & Lesk, 1986</json:string><json:string>Witherell & Uhlenbeck, 1989</json:string><json:string>Valegard et al., 1990</json:string><json:string>Ni et al., 1996</json:string><json:string>Hohn, 1969b</json:string><json:string>Stockley et al., 1993</json:string><json:string>Spingola & Peabody, 1997</json:string><json:string>Gott et al., 1991</json:string><json:string>Stonehouse & Stockley, 1993</json:string><json:string>Brunger, 1990</json:string><json:string>Knolle & Hohn, 1975</json:string><json:string>Hung et al., 1969</json:string><json:string>Hohn, 1969a</json:string><json:string>Fiers, 1979</json:string><json:string>Kraulis, 1991</json:string><json:string>Valegard et al., 1994</json:string><json:string>Golmohammadi et al., 1993</json:string><json:string>Witherell et al., 1991</json:string><json:string>Stonehouse et al., 1996a,b</json:string><json:string>Valegard et al., 1994, 1997</json:string><json:string>Inokuchi et al., 1986</json:string><json:string>Beckett et al., 1988</json:string><json:string>Ni et al., 1995, 1996</json:string><json:string>LeCuyer et al., 1995</json:string><json:string>Dhaese et al., 1980</json:string><json:string>Lim et al., 1996</json:string><json:string>Zinder, 1975</json:string></ref_bibl><bibl></bibl></unitex></namedEntities><ark><json:string>ark:/67375/6H6-2HL7QSCZ-Q</json:string></ark><categories><wos><json:string>1 - science</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 - biochemistry & molecular biology</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></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 - psychologie. psychophysiologie</json:string></inist></categories><publicationDate>1997</publicationDate><copyrightDate>1997</copyrightDate><doi><json:string>10.1006/jmbi.1997.1214</json:string></doi><id>700B1758131F103787DB2DB48B8FBF2612F3DE45</id><score>1</score><fulltext><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-2HL7QSCZ-Q/fulltext.pdf</uri></json:item><json:item><extension>zip</extension><original>false</original><mimetype>application/zip</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-2HL7QSCZ-Q/bundle.zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/ark:/67375/6H6-2HL7QSCZ-Q/fulltext.tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main" xml:lang="en">The crystal structure of bacteriophage GA and a comparison of bacteriophages belonging to the major groups of Escherichia coli leviviruses</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher scheme="https://scientific-publisher.data.istex.fr">ELSEVIER</publisher><availability><licence><p>©1997 Academic Press</p></licence><p scheme="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-HKKZVM7B-M">elsevier</p></availability><date>1997</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>Edited by K. Nagai</note><note type="content">Section title: Regular article</note><note type="content">Figure 1: GA hexamer. The three subunits A, B and C in the icosahedral asymmetric unit (e.g. a triangle limited by the 5-fold and two 3-fold axes) are shown in yellow, green and blue, respectively, and the three subunits B′, A′ and C′ completing the dimers are shown in the corresponding pale colours. The FG loops of further subunits, completing the interactions at the 5-fold and 3-fold (quasi-6-fold) axes are also shown. The inset shows an icosahedron in the same orientation. Below is a C subunit which shows the denotation of the secondary structure elements. Figures 1 to 6 and 9 were produced with the program MOLSCRIPT (Kraulis, 1991).</note><note type="content">Figure 2: Stereo view of Cα traces of AB′ dimers of GA (black), MS2 (green) and Qβ (blue).</note><note type="content">Figure 3: Differences between the C to N-terminal intra-dimer interactions in the AB′ dimer of MS2 and GA. Subunit A is in yellow and subunit B in green.</note><note type="content">Figure 4: The icosahedral asymmetric unit of phage GA, showing the only completely conserved interaction among the investigated phages, keeping the dimers together. Enlarged plots for Qβ, MS2 and GA are shown.</note><note type="content">Figure 5: The interactions along the 5-fold and quasi-6-fold axes, connecting the FG loops. For details of the inter-dimer interactions see Table 4. The FG loop of the A and C subunits in Qβ are disordered and not modelled for residues 69 to 75.</note><note type="content">Figure 6: Possible assembly pathway of the GA particle. Top, two dimers interact. The B conformation of the FG loop might or might not be induced at this stage. Middle, a pentamer of dimers in AB′ conformation is formed. Bottom, a dimer in CC′ conformation is added.</note><note type="content">Figure 9: Top, Cα tracing of an AB′ dimer showing the position of residues involved in specific RNA binding as defined by the MS2-RNA complex. Bottom, stereo view of superimposed RNA binding sites of GA (blue) and MS2 (green). The RNA molecule from the MS2 complex is included in the Figure.</note><note type="content">Figure 7: The translational operators of MS2, GA and Qβ (a) and their minimal requirements (b).</note><note type="content">Figure 8: Diagram showing conserved and variable amino acid residues at the RNA binding sites of MS2, GA and Qβ.</note><note type="content">Figure 10: Amino acid sequence of phages and the role of side-chains. Columns 1 to 4 show the sequences of MS2, fr, GA and Qβ, respectively; column 5 shows the consensus sequence for all coliphages; columns 6 and 7 show the sequences of PRR1 and PP7, respectively; and column 8 shows the consensus for all leviviruses. Numbering is according to MS2 throughout. The GA sequence is the one observed in the crystal, which differs from the published sequence at positions 59 and 79. The colouring scheme for the sequences is green for hydrophobic (W, F, Y, M, I, L, V), cyan for small non-polar (P, A, G, C), blue for non-charged polar (S, T, N, Q, H), red for negatively charged (D, E) and magenta for positively charged (R, K) side-chains. The next column shows the secondary structure elements. The last four columns, also labelled 1 to 4, show the exposure of, and contacts made by, the side-chains in the four known structures. The letters stand for: c, core of subunit; o, outer surface; r, inner surface; d, dimer interface; i, inter-dimer contacts; b, both dimer and inter-dimer contacts. Capital letters D, I and B are used when the interaction involves a polar contact, and capital R is used for the direct RNA interaction as defined by the MS2-operator complex. The symbols for exposed side-chains are used for those side-chains not involved in subunit-subunit interactions. Some side-chains have different roles in different subunits; for example, residues 40, 66, 70 and 76.</note><note type="content">Table 1: Comparison of the phage structures. Rms differences (in Å) between superimposed Cα coordinates</note><note type="content">Table 2: Polar interactions within the monomer</note><note type="content">Table 3: Polar subunit interactions in the dimer</note><note type="content">Table 4: Polar interactions between the dimers</note><note type="content">Table 5: Scaling R-factor and degree of completeness as a function of resolution</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">The crystal structure of bacteriophage GA and a comparison of bacteriophages belonging to the major groups of Escherichia coli leviviruses</title><author xml:id="author-0000"><persName><forename type="first">Kaspars</forename><surname>Tars</surname></persName><affiliation>Biomedical Research and Study Centre, Latvian University, Ratsupites 1, Riga, Latvia</affiliation></author><author xml:id="author-0001"><persName><forename type="first">Maija</forename><surname>Bundule</surname></persName><affiliation>Biomedical Research and Study Centre, Latvian University, Ratsupites 1, Riga, Latvia</affiliation></author><author xml:id="author-0002"><persName><forename type="first">Kerstin</forename><surname>Fridborg</surname></persName><affiliation>Department of Molecular Biology Uppsala University Box 590, S-751 24 Uppsala, Sweden</affiliation></author><author xml:id="author-0003"><persName><forename type="first">Lars</forename><surname>Liljas</surname></persName><note type="correspondence"><p>Corresponding author</p></note><affiliation>Department of Molecular Biology Uppsala University Box 590, S-751 24 Uppsala, Sweden</affiliation></author><idno type="istex">700B1758131F103787DB2DB48B8FBF2612F3DE45</idno><idno type="ark">ark:/67375/6H6-2HL7QSCZ-Q</idno><idno type="DOI">10.1006/jmbi.1997.1214</idno><idno type="PII">S0022-2836(97)91214-6</idno></analytic><monogr><title level="j">Journal of Molecular Biology</title><title level="j" type="abbrev">YJMBI</title><idno type="pISSN">0022-2836</idno><idno type="PII">S0022-2836(00)X0097-6</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="1997"></date><biblScope unit="volume">271</biblScope><biblScope unit="issue">5</biblScope><biblScope unit="page" from="759">759</biblScope><biblScope unit="page" to="773">773</biblScope></imprint></monogr></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>1997</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>Abstract: The three-dimensional structure of the small T = 3 RNA bacteriophage GA has been determined at 3.4 Å resolution. The structure was solved by molecular replacement, using the phage MS2 as an initial model. A comparison of the protein shells of the four related phages GA, MS2, fr and Qβ was carried out in order to define structural features of particular importance for their assembly and specific RNA interaction. A high degree of similarity was found in the RNA binding sites, whereas larger structural differences are located in the loop regions of the coat proteins, especially in the FG loops forming 5-fold and quasi-6-fold contacts. The overall arrangement of the protein subunits in the shells of these phages is very similar, although the details of the interactions differ. The few conserved interactions are suggested to govern the subunit packing during assembly.</p></abstract><textClass><keywords scheme="keyword"><list><head>article-category</head><item><term>Regular article</term></item></list></keywords></textClass><textClass xml:lang="en"><keywords scheme="keyword"><list><head>Keywords</head><item><term>MS2</term></item><item><term>GA</term></item><item><term>Qβ</term></item><item><term>virus assembly</term></item><item><term>virus evolution</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="1997-06-04">Modified</change><change when="1997">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-2HL7QSCZ-Q/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:entity SYSTEM="gr7" NDATA="IMAGE" name="GR7"></istex:entity><istex:entity SYSTEM="gr8" NDATA="IMAGE" name="GR8"></istex:entity><istex:entity SYSTEM="gr9" NDATA="IMAGE" name="GR9"></istex:entity><istex:entity SYSTEM="gr10" NDATA="IMAGE" name="GR10"></istex:entity></istex:docType><istex:document><converted-article version="4.5.2" docsubtype="fla" xml:lang="en"><item-info><jid>YJMBI</jid><aid>91214</aid><ce:pii>S0022-2836(97)91214-6</ce:pii><ce:doi>10.1006/jmbi.1997.1214</ce:doi><ce:copyright type="full-transfer" year="1997">Academic Press</ce:copyright><ce:doctopics><ce:doctopic><ce:text>Regular article</ce:text></ce:doctopic></ce:doctopics></item-info><head><ce:dochead><ce:textfn>Regular article</ce:textfn></ce:dochead><ce:title>The crystal structure of bacteriophage GA and a comparison of bacteriophages belonging to the major groups of <ce:italic>Escherichia coli</ce:italic> leviviruses<ce:cross-ref refid="FN1"><ce:sup>1</ce:sup></ce:cross-ref><ce:footnote id="FN1"><ce:label>1</ce:label><ce:note-para><ce:bold><ce:italic>Edited by K. Nagai</ce:italic></ce:bold></ce:note-para></ce:footnote></ce:title><ce:author-group><ce:author><ce:given-name>Kaspars</ce:given-name><ce:surname>Tars</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>1</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Maija</ce:given-name><ce:surname>Bundule</ce:surname><ce:cross-ref refid="AFF1"><ce:sup>1</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Kerstin</ce:given-name><ce:surname>Fridborg</ce:surname><ce:cross-ref refid="AFF2"><ce:sup>2</ce:sup></ce:cross-ref></ce:author><ce:author><ce:given-name>Lars</ce:given-name><ce:surname>Liljas</ce:surname><ce:cross-ref refid="AFF2"><ce:sup>2</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>Biomedical Research and Study Centre, Latvian University, Ratsupites 1, Riga, Latvia</ce:textfn></ce:affiliation><ce:affiliation id="AFF2"><ce:label>2</ce:label><ce:textfn>Department of Molecular Biology Uppsala University Box 590, S-751 24 Uppsala, Sweden</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="17" month="2" year="1997"></ce:date-received><ce:date-revised day="4" month="6" year="1997"></ce:date-revised><ce:date-accepted day="14" month="6" year="1997"></ce:date-accepted><ce:abstract><ce:section-title>Abstract</ce:section-title><ce:abstract-sec><ce:simple-para>The three-dimensional structure of the small <ce:italic>T</ce:italic> = 3 RNA bacteriophage GA has been determined at 3.4 Å resolution. The structure was solved by molecular replacement, using the phage MS2 as an initial model. A comparison of the protein shells of the four related phages GA, MS2, fr and Qβ was carried out in order to define structural features of particular importance for their assembly and specific RNA interaction. A high degree of similarity was found in the RNA binding sites, whereas larger structural differences are located in the loop regions of the coat proteins, especially in the FG loops forming 5-fold and quasi-6-fold contacts. The overall arrangement of the protein subunits in the shells of these phages is very similar, although the details of the interactions differ. The few conserved interactions are suggested to govern the subunit packing during assembly.</ce:simple-para></ce:abstract-sec></ce:abstract><ce:keywords><ce:section-title>Keywords</ce:section-title><ce:keyword><ce:text>MS2</ce:text></ce:keyword><ce:keyword><ce:text>GA</ce:text></ce:keyword><ce:keyword><ce:text>Qβ</ce:text></ce:keyword><ce:keyword><ce:text>virus assembly</ce:text></ce:keyword><ce:keyword><ce:text>virus evolution</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 bacteriophage GA and a comparison of bacteriophages belonging to the major groups of Escherichia coli leviviruses</title></titleInfo><titleInfo type="alternative" lang="en" contentType="CDATA"><title>The crystal structure of bacteriophage GA and a comparison of bacteriophages belonging to the major groups of</title></titleInfo><name type="personal"><namePart type="given">Kaspars</namePart><namePart type="family">Tars</namePart><affiliation>Biomedical Research and Study Centre, Latvian University, Ratsupites 1, Riga, Latvia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Maija</namePart><namePart type="family">Bundule</namePart><affiliation>Biomedical Research and Study Centre, Latvian University, Ratsupites 1, Riga, Latvia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Kerstin</namePart><namePart type="family">Fridborg</namePart><affiliation>Department of Molecular Biology Uppsala University Box 590, S-751 24 Uppsala, Sweden</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Lars</namePart><namePart type="family">Liljas</namePart><affiliation>Department of Molecular Biology Uppsala University Box 590, S-751 24 Uppsala, Sweden</affiliation><description>Corresponding author</description><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">1997</dateIssued><dateModified encoding="w3cdtf">1997-06-04</dateModified><copyrightDate encoding="w3cdtf">1997</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><abstract lang="en">Abstract: The three-dimensional structure of the small T = 3 RNA bacteriophage GA has been determined at 3.4 Å resolution. The structure was solved by molecular replacement, using the phage MS2 as an initial model. A comparison of the protein shells of the four related phages GA, MS2, fr and Qβ was carried out in order to define structural features of particular importance for their assembly and specific RNA interaction. A high degree of similarity was found in the RNA binding sites, whereas larger structural differences are located in the loop regions of the coat proteins, especially in the FG loops forming 5-fold and quasi-6-fold contacts. The overall arrangement of the protein subunits in the shells of these phages is very similar, although the details of the interactions differ. The few conserved interactions are suggested to govern the subunit packing during assembly.</abstract><note type="footnote">Edited by K. Nagai</note><note type="content">Section title: Regular article</note><note type="content">Figure 1: GA hexamer. The three subunits A, B and C in the icosahedral asymmetric unit (e.g. a triangle limited by the 5-fold and two 3-fold axes) are shown in yellow, green and blue, respectively, and the three subunits B′, A′ and C′ completing the dimers are shown in the corresponding pale colours. The FG loops of further subunits, completing the interactions at the 5-fold and 3-fold (quasi-6-fold) axes are also shown. The inset shows an icosahedron in the same orientation. Below is a C subunit which shows the denotation of the secondary structure elements. Figures 1 to 6 and 9 were produced with the program MOLSCRIPT (Kraulis, 1991).</note><note type="content">Figure 2: Stereo view of Cα traces of AB′ dimers of GA (black), MS2 (green) and Qβ (blue).</note><note type="content">Figure 3: Differences between the C to N-terminal intra-dimer interactions in the AB′ dimer of MS2 and GA. Subunit A is in yellow and subunit B in green.</note><note type="content">Figure 4: The icosahedral asymmetric unit of phage GA, showing the only completely conserved interaction among the investigated phages, keeping the dimers together. Enlarged plots for Qβ, MS2 and GA are shown.</note><note type="content">Figure 5: The interactions along the 5-fold and quasi-6-fold axes, connecting the FG loops. For details of the inter-dimer interactions see Table 4. The FG loop of the A and C subunits in Qβ are disordered and not modelled for residues 69 to 75.</note><note type="content">Figure 6: Possible assembly pathway of the GA particle. Top, two dimers interact. The B conformation of the FG loop might or might not be induced at this stage. Middle, a pentamer of dimers in AB′ conformation is formed. Bottom, a dimer in CC′ conformation is added.</note><note type="content">Figure 9: Top, Cα tracing of an AB′ dimer showing the position of residues involved in specific RNA binding as defined by the MS2-RNA complex. Bottom, stereo view of superimposed RNA binding sites of GA (blue) and MS2 (green). The RNA molecule from the MS2 complex is included in the Figure.</note><note type="content">Figure 7: The translational operators of MS2, GA and Qβ (a) and their minimal requirements (b).</note><note type="content">Figure 8: Diagram showing conserved and variable amino acid residues at the RNA binding sites of MS2, GA and Qβ.</note><note type="content">Figure 10: Amino acid sequence of phages and the role of side-chains. Columns 1 to 4 show the sequences of MS2, fr, GA and Qβ, respectively; column 5 shows the consensus sequence for all coliphages; columns 6 and 7 show the sequences of PRR1 and PP7, respectively; and column 8 shows the consensus for all leviviruses. Numbering is according to MS2 throughout. The GA sequence is the one observed in the crystal, which differs from the published sequence at positions 59 and 79. The colouring scheme for the sequences is green for hydrophobic (W, F, Y, M, I, L, V), cyan for small non-polar (P, A, G, C), blue for non-charged polar (S, T, N, Q, H), red for negatively charged (D, E) and magenta for positively charged (R, K) side-chains. The next column shows the secondary structure elements. The last four columns, also labelled 1 to 4, show the exposure of, and contacts made by, the side-chains in the four known structures. The letters stand for: c, core of subunit; o, outer surface; r, inner surface; d, dimer interface; i, inter-dimer contacts; b, both dimer and inter-dimer contacts. Capital letters D, I and B are used when the interaction involves a polar contact, and capital R is used for the direct RNA interaction as defined by the MS2-operator complex. The symbols for exposed side-chains are used for those side-chains not involved in subunit-subunit interactions. Some side-chains have different roles in different subunits; for example, residues 40, 66, 70 and 76.</note><note type="content">Table 1: Comparison of the phage structures. Rms differences (in Å) between superimposed Cα coordinates</note><note type="content">Table 2: Polar interactions within the monomer</note><note type="content">Table 3: Polar subunit interactions in the dimer</note><note type="content">Table 4: Polar interactions between the dimers</note><note type="content">Table 5: Scaling R-factor and degree of completeness as a function of resolution</note><subject><genre>article-category</genre><topic>Regular article</topic></subject><subject lang="en"><genre>Keywords</genre><topic>MS2</topic><topic>GA</topic><topic>Qβ</topic><topic>virus assembly</topic><topic>virus evolution</topic></subject><relatedItem type="host"><titleInfo><title>Journal of Molecular Biology</title></titleInfo><titleInfo type="abbreviated"><title>YJMBI</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">1997</dateIssued></originInfo><identifier type="ISSN">0022-2836</identifier><identifier type="PII">S0022-2836(00)X0097-6</identifier><part><date>1997</date><detail type="volume"><number>271</number><caption>vol.</caption></detail><detail type="issue"><number>5</number><caption>no.</caption></detail><extent unit="issue-pages"><start>671</start><end>845</end></extent><extent unit="pages"><start>759</start><end>773</end></extent></part></relatedItem><identifier type="istex">700B1758131F103787DB2DB48B8FBF2612F3DE45</identifier><identifier type="ark">ark:/67375/6H6-2HL7QSCZ-Q</identifier><identifier type="DOI">10.1006/jmbi.1997.1214</identifier><identifier type="PII">S0022-2836(97)91214-6</identifier><accessCondition type="use and reproduction" contentType="copyright">©1997 Academic Press</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>Academic Press, ©1997</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-2HL7QSCZ-Q/record.json</uri></json:item></metadata></istex></record>Pour manipuler ce document sous Unix (Dilib)
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