Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.00 kDa 
• Atom Count: 1296 
• Modelled Residue Count: 46 
• Deposited Residue Count: 46 
• Unique nucleic acid chains: 1

462D

CRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITE

• PDB DOI: 10.2210/pdb462D/pdb
• NDB: UR0005

• Classification: RNA
• Mutation(s): No 


• Deposited: 1999-03-18 Released: 1999-12-02 
• Deposition Author(s): Ennifar, E., Yusupov, M., Walter, P., Marquet, R., Ehresmann, C., Ehresmann, B., Dumas, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.212 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 

Literature

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.

(1999) Structure 7: 1439-1449

• PubMed: 10574792 
• DOI: 10.1016/s0969-2126(00)80033-7
• Primary Citation of Related Structures:  
  1Y99, 462D


• PubMed Abstract: 
  

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.

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Organizational Affiliation: 

UPR9002 - Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg cedex, F-67084, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G) -3')	A, B	23	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.212 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.1	α = 90
b = 59.1	β = 90
c = 64	γ = 120

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-03-18 
• Released Date: 1999-12-02 
Deposition Author(s): Ennifar, E., Yusupov, M., Walter, P., Marquet, R., Ehresmann, C., Ehresmann, B., Dumas, P.

Revision History  

• Version 1.0: 1999-12-02
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance