1xpf
From Proteopedia
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|PDB= 1xpf |SIZE=350|CAPTION= <scene name='initialview01'>1xpf</scene>, resolution 2.30Å | |PDB= 1xpf |SIZE=350|CAPTION= <scene name='initialview01'>1xpf</scene>, resolution 2.30Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1xp7|1XP7]], [[1xpe|1XPE]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xpf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xpf OCA], [http://www.ebi.ac.uk/pdbsum/1xpf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xpf RCSB]</span> | ||
}} | }} | ||
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[[Category: Dumas, P.]] | [[Category: Dumas, P.]] | ||
[[Category: Ennifar, E.]] | [[Category: Ennifar, E.]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: NA]] | ||
| - | [[Category: SO4]] | ||
| - | [[Category: SPM]] | ||
[[Category: hiv-1]] | [[Category: hiv-1]] | ||
[[Category: loop-loop complex]] | [[Category: loop-loop complex]] | ||
[[Category: rna]] | [[Category: rna]] | ||
| - | ''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 00:52:49 2008'' |
Revision as of 21:52, 30 March 2008
| |||||||
| , resolution 2.30Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , | ||||||
| Related: | 1XP7, 1XPE
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
HIV-1 subtype A genomic RNA Dimerization Initiation Site
Overview
All retroviruses encapsidate their genome as a dimer of homologous single-stranded RNAs. The dimerization initiation site (DIS) of human immunodeficiency virus type 1 (HIV-1) is located in the 5'-untranslated region of the viral genome and consists of a hairpin with a 6 nt self-complementary loop sequence. Genomic RNA dimerization, a crucial step for virion infectivity, is promoted by the formation of a loop-loop complex (or kissing complex) between two DIS hairpins. Crystal structures for the subtypes A, B and F of the HIV-1 DIS kissing complex have now been solved at 2.3 A, 1.9 A and 1.6 A, respectively. They revealed a polymorphism of bulged-out residues showing clearly that their conformation is not a mere consequence of crystal packing. They also provide more insights into ion binding, hydration, and RNA conformation and flexibility. In particular, we observed the binding of spermine to the loop-loop helix, which displaced a magnesium cation important for subtype A DIS dimerization. The excellent agreement between X-ray structures and the results of chemical probing and interference data on larger viral RNA fragments shows that the crystal structures are relevant for the DIS kissing complex present in solution and in viral particles. Accordingly, these structures will be helpful for designing new drugs derived from aminoglycoside antibiotics and targeted against the RNA dimerization step of the viral life-cycle.
About this Structure
1XPF is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Polymorphism of bulged-out residues in HIV-1 RNA DIS kissing complex and structure comparison with solution studies., Ennifar E, Dumas P, J Mol Biol. 2006 Feb 24;356(3):771-82. Epub 2005 Dec 21. PMID:16403527
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