1DUQ

CRYSTAL STRUCTURE OF THE REV BINDING ELEMENT OF HIV-1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability.

Hung, L.W., Holbrook, E.L., Holbrook, S.R.

(2000) Proc Natl Acad Sci U S A 97: 5107-5112

  • DOI: 10.1073/pnas.090588197
  • Primary Citation of Related Structures:  
    1DUQ

  • PubMed Abstract: 

    • The crystal and molecular structure of an RNA duplex corresponding to the high affinity Rev protein binding element (RBE) has been determined at 2.1-A resolution. Four unique duplexes are present in the crystal, comprising two structural variants. In each duplex, the RNA double helix consists of an annealed 12-mer and 14-mer that form an asymmetric internal loop consisting of G-G and G-A noncanonical base pairs and a flipped-out uridine ...

    The crystal and molecular structure of an RNA duplex corresponding to the high affinity Rev protein binding element (RBE) has been determined at 2.1-A resolution. Four unique duplexes are present in the crystal, comprising two structural variants. In each duplex, the RNA double helix consists of an annealed 12-mer and 14-mer that form an asymmetric internal loop consisting of G-G and G-A noncanonical base pairs and a flipped-out uridine. The 12-mer strand has an A-form conformation, whereas the 14-mer strand is distorted to accommodate the bulges and noncanonical base pairing. In contrast to the NMR model of the unbound RBE, an asymmetric G-G pair with N2-N7 and N1-O6 hydrogen bonding, is formed in each helix. The G-A base pairing agrees with the NMR structure in one structural variant, but forms a novel water-mediated pair in the other. A backbone flip and reorientation of the G-G base pair is required to assume the RBE conformation present in the NMR model of the complex between the RBE and the Rev peptide.

    Organizational Affiliation: 

    Macromolecular Crystallography Facility and Structural Biology Department, Melvin Calvin Building, Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA.



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
THE REV BINDING ELEMENTA, C, E, G 12N/A
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
THE REV BINDING ELEMENTB, D, F, H 14N/A
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.993α = 114.52
b = 53.93β = 89.88
c = 64.729γ = 102.85
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance