4B3O

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: 3.30 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.276 

wwPDB Validation 3D Report Full Report


This is version 1.4 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
  • Structures With Same Primary Citation

  • 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 1Mutation(s): 7 
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.4.23.16 (PDB Primary Data), 3.1.13.2 (PDB Primary Data), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
P51 RT
B
441Human immunodeficiency virus 1Mutation(s): 3 
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.4.23.16 (PDB Primary Data), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*GP*TP*AP*TP*GP*CP*CP*TP*AP*TP*AP*GP*TP *TP*AP*TP*TP*GP*TP*GP*GP*CP*C)-3'D24synthetic construct

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 4
MoleculeChainsLengthOrganism
5'-R(*AP*UP*GP*AP*3DRP*GP*GP*CP*CP*AP*CP*AP*AP*UP*AP *AP*CP*UP*AP*UP*AP*GP*GP*CP*AP*UP*A)-3'R27synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EFZ
Query on EFZ

Download CCD File 
A
(-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE
C14 H9 Cl F3 N O2
XPOQHMRABVBWPR-ZDUSSCGKSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
D, R
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.276 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.598α = 90
b = 164.598β = 90
c = 129.03γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Database references
  • Version 1.2: 2013-02-20
    Changes: Database references
  • Version 1.3: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2019-05-15
    Changes: Data collection, Experimental preparation