462d
From Proteopedia
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|PDB= 462d |SIZE=350|CAPTION= <scene name='initialview01'>462d</scene>, resolution 2.30Å | |PDB= 462d |SIZE=350|CAPTION= <scene name='initialview01'>462d</scene>, resolution 2.30Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=462d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=462d OCA], [http://www.ebi.ac.uk/pdbsum/462d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=462d RCSB]</span> | ||
}} | }} | ||
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[[Category: Walter, P.]] | [[Category: Walter, P.]] | ||
[[Category: Yusupov, M.]] | [[Category: Yusupov, M.]] | ||
| - | [[Category: MG]] | ||
[[Category: bulge]] | [[Category: bulge]] | ||
[[Category: hiv]] | [[Category: hiv]] | ||
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[[Category: rna duplex]] | [[Category: rna duplex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:37:31 2008'' |
Revision as of 02:37, 31 March 2008
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| , resolution 2.30Å | |||||||
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITE
Overview
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 A 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.
About this Structure
462D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges., Ennifar E, Yusupov M, Walter P, Marquet R, Ehresmann B, Ehresmann C, Dumas P, Structure. 1999 Nov 15;7(11):1439-49. PMID:10574792
Page seeded by OCA on Mon Mar 31 05:37:31 2008
Categories: Protein complex | Dumas, P. | Ehresmann, B. | Ehresmann, C. | Ennifar, E. | Marquet, R. | Walter, P. | Yusupov, M. | Bulge | Hiv | Magnesium binding | Mismatch | Rna duplex
