4B3P

Structures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Conformation and Substrate Interface


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.839 Å
  • R-Value Free: 0.404 
  • R-Value Work: 0.364 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Complexes of HIV-1 RT, Nnrti and RNA/DNA Hybrid Reveal a Structure Compatible with RNA Degradation

Lapkouski, M.Tian, L.Miller, J.T.Le Grice, S.F.J.Yang, W.

(2013) Nat.Struct.Mol.Biol. 20: 230

  • DOI: 10.1038/nsmb.2485
  • Primary Citation of Related Structures:  4B3O, 4B3Q

  • PubMed Abstract: 
  • Hundreds of structures of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase (RT) have been determined, but only one contains an RNA/DNA hybrid. Here we report three structures of HIV-1 RT complexed with a non-nucleotide RT inhibitor ( ...

    Hundreds of structures of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase (RT) have been determined, but only one contains an RNA/DNA hybrid. Here we report three structures of HIV-1 RT complexed with a non-nucleotide RT inhibitor (NNRTI) and an RNA/DNA hybrid. In the presence of an NNRTI, the RNA/DNA structure differs from all prior nucleic acid-RT structures including the RNA/DNA hybrid. The enzyme structure also differs from all previous RT-DNA complexes. Thus, the hybrid has ready access to the RNase-H active site. These observations indicate that an RT-nucleic acid complex may adopt two structural states, one competent for DNA polymerization and the other for RNA degradation. RT mutations that confer drug resistance but are distant from the inhibitor-binding sites often map to the unique RT-hybrid interface that undergoes conformational changes between two catalytic states.


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
REVERSE TRANSCRIPTASE/RIBONUCLEASE H
A
560Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
P51 RT
B
454Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Entity ID: 3
MoleculeChainsLengthOrganism
DNAD29synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
RNAR34synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
N
Query on N
R
RNA LINKINGC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.839 Å
  • R-Value Free: 0.404 
  • R-Value Work: 0.364 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 163.000α = 90.00
b = 163.000β = 90.00
c = 229.600γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references
  • Version 1.2: 2013-02-20
    Type: Database references