3K2P

HIV-1 Reverse Transcriptase Isolated RnaseH Domain with the Inhibitor beta-thujaplicinol Bound at the Active Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

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This is version 1.2 of the entry. See complete history


Literature

Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site.

Himmel, D.M.Maegley, K.A.Pauly, T.A.Bauman, J.D.Das, K.Dharia, C.Clark, A.D.Ryan, K.Hickey, M.J.Love, R.A.Hughes, S.H.Bergqvist, S.Arnold, E.

(2009) Structure 17: 1625-1635

  • DOI: https://doi.org/10.1016/j.str.2009.09.016
  • Primary Citation of Related Structures:  
    3IG1, 3K2P

  • PubMed Abstract: 

    Novel inhibitors are needed to counteract the rapid emergence of drug-resistant HIV variants. HIV-1 reverse transcriptase (RT) has both DNA polymerase and RNase H (RNH) enzymatic activities, but approved drugs that inhibit RT target the polymerase. Inhibitors that act against new targets, such as RNH, should be effective against all of the current drug-resistant variants. Here, we present 2.80 A and 2.04 A resolution crystal structures of an RNH inhibitor, beta-thujaplicinol, bound at the RNH active site of both HIV-1 RT and an isolated RNH domain. beta-thujaplicinol chelates two divalent metal ions at the RNH active site. We provide biochemical evidence that beta-thujaplicinol is a slow-binding RNH inhibitor with noncompetitive kinetics and suggest that it forms a tropylium ion that interacts favorably with RT and the RNA:DNA substrate.


  • Organizational Affiliation

    Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8021, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reverse Transcriptase
A, B
136Human immunodeficiency virus type 1 BH10Mutation(s): 0 
Gene Names: gag-pol
EC: 3.1.26.4
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.143α = 90
b = 51.143β = 90
c = 112.435γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations