1CSL

CRYSTAL STRUCTURE OF THE RRE HIGH AFFINITY SITE

• PDB DOI: https://doi.org/10.2210/pdb1CSL/pdb
• NAKB: 1CSL

• Classification: RNA
• Mutation(s): No 


• Deposited: 1999-08-18 Released: 2000-02-14 
• Deposition Author(s): Ippolito, J.A., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.241 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 

Literature

The structure of the HIV-1 RRE high affinity rev binding site at 1.6 A resolution.

Ippolito, J.A., Steitz, T.A.

(2000) J Mol Biol 295: 711-717

• PubMed: 10656783 
• DOI: https://doi.org/10.1006/jmbi.1999.3405
• Primary Citation of Related Structures:  
  1CSL


• PubMed Abstract: 
  

  The crystal structure of a 28 nt RNA fragment containing the human immunodeficiency virus type 1 (HIV-1) Rev response element high affinity binding site for Rev protein has been solved at 1.6 A resolution. The overall structure of the RRE helix is greatly distorted from A-form geometry by the presence of two purine-purine base-pairs and two single nucleotide bulges. G48 and G71 form a Hoogsteen-type asymmetric base-pair with G71 adopting a syn conformation. The non-canonical regions in the unliganded Rev response element molecule narrow the major groove width with respect to standard A-RNA. The Rev response element structure observed here represents a closed form of the Rev binding site and differs from conformations of the RNA observed previously by solution NMR studies.

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Organizational Affiliation: 

Department of Molecular Biophysics, Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.99 kDa 
• Atom Count: 739 
• Modelled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*AP*AP*CP*GP*GP*GP*CP*GP*CP*AP*GP*AP*A)-3'	A	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*UP*CP*UP*GP*AP*CP*GP*GP*UP*AP*CP*GP*UP*UP*U)-3'	B	15	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.241 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.5	α = 90
b = 24.3	β = 116.7
c = 46.1	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-02-14 
Deposition Author(s): Ippolito, J.A., Steitz, T.A.

Revision History  

• Version 1.0: 2000-02-14
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-12-28
  Changes: Advisory
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references