4B3Q

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: 5.00 Å
  • R-Value Free: 0.407 
  • R-Value Work: 0.361 
  • R-Value Observed: 0.363 

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This is version 1.3 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: https://doi.org/10.1038/nsmb.2485
  • Primary Citation of Related Structures:  
    4B3O, 4B3P, 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 (NNRTI) and an RNA/DNA hybrid ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
REVERSE TRANSCRIPTASE/RIBONUCLEASE HA560Human 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), 3.1.13.2 (PDB Primary Data), 3.4.23.16 (PDB Primary Data), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
P51 RTB454Human immunodeficiency virus 1Mutation(s): 3 
EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
PRIMER DNAC [auth D]25synthetic construct
Protein Feature View
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Entity ID: 4
MoleculeChainsLengthOrganismImage
TEMPLATE RNAD [auth R]34synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NVP
Query on NVP
Download Ideal Coordinates CCD File 
E [auth A]11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE
C15 H14 N4 O
NQDJXKOVJZTUJA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.00 Å
  • R-Value Free: 0.407 
  • R-Value Work: 0.361 
  • R-Value Observed: 0.363 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 272.7α = 90
b = 272.7β = 90
c = 233.1γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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, Experimental preparation, Other, Source and taxonomy