MersV1, Main, Exploration, bibRecord, 003882

The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges

Identifieur interne : 003882 ( Main/Exploration ); précédent : 003881; suivant : 003883

The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges

Auteurs : E. Ennifar [France] ; M. Yusupov [États-Unis] ; P. Walter [France] ; R. Marquet [France] ; B. Ehresmann [France] ; C. Ehresmann [France] ; P. Dumas [France]

Source :

Structure [ 0969-2126 ] ; 1999.

RBID : ISTEX:8ADDDDEEB5354C735EB0B8C66632BCC1D7056659

English descriptors

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:

https://api.istex.fr/ark:/67375/6H6-KTKZ2JJP-T/fulltext.pdf

DOI: 10.1016/S0969-2126(00)80033-7

Affiliations:

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<term>magnesium</term>
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<keywords scheme="Teeft" xml:lang="en"><term>Acta</term>
<term>Acta crystallogr</term>
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<term>Adenine base</term>
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<term>Alternate conformations</term>
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<term>Base pair</term>
<term>Base pairs</term>
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<term>Bulge</term>
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<term>Cell parameters</term>
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<term>Crystal structures</term>
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<term>Crystallization process</term>
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<term>Data collection</term>
<term>Data collection summary</term>
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<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>
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<term>Extrahelical bulges</term>
<term>Extrahelical conformation</term>
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<term>Fourier difference maps</term>
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<term>Hammerhead ribozyme</term>
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<term>Methods enzymol</term>
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<term>Nucleic acids</term>
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<term>Positive peaks</term>
<term>Previous results</term>
<term>Redundancy number</term>
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<term>Reflections rsym</term>
<term>Research article dimerization site</term>
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<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>
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The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges

The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges

Source :

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri