3V81

Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and the nonnucleoside inhibitor nevirapine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8503 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.

Das, K.Martinez, S.E.Bauman, J.D.Arnold, E.

(2012) Nat.Struct.Mol.Biol. 19: 253-259

  • DOI: 10.1038/nsmb.2223
  • Primary Citation of Related Structures:  
  • Also Cited By: 4G1Q, 5I3U, 4R5P, 4Q0B, 4PWD, 4PUO, 4PQU

  • PubMed Abstract: 
  • Combinations of nucleoside and non-nucleoside inhibitors (NNRTIs) of HIV-1 reverse transcriptase (RT) are widely used in anti-AIDS therapies. Five NNRTIs, including nevirapine, are clinical drugs; however, the molecular mechanism of inhibition by NNR ...

    Combinations of nucleoside and non-nucleoside inhibitors (NNRTIs) of HIV-1 reverse transcriptase (RT) are widely used in anti-AIDS therapies. Five NNRTIs, including nevirapine, are clinical drugs; however, the molecular mechanism of inhibition by NNRTIs is not clear. We determined the crystal structures of RT-DNA-nevirapine, RT-DNA, and RT-DNA-AZT-triphosphate complexes at 2.85-, 2.70- and 2.80-Å resolution, respectively. The RT-DNA complex in the crystal could bind nevirapine or AZT-triphosphate but not both. Binding of nevirapine led to opening of the NNRTI-binding pocket. The pocket formation caused shifting of the 3' end of the DNA primer by ~5.5 Å away from its polymerase active site position. Nucleic acid interactions with fingers and palm subdomains were reduced, the dNTP-binding pocket was distorted and the thumb opened up. The structures elucidate complementary roles of nucleoside and non-nucleoside inhibitors in inhibiting RT.


    Related Citations: 
    • Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants.
      Das, K.,Clark, A.D.,Lewi, P.J.,Heeres, J.,De Jonge, M.R.,Koymans, L.M.,Vinkers, H.M.,Daeyaert, F.,Ludovici, D.W.,Kukla, M.J.,De Corte, B.,Kavash, R.W.,Ho, C.Y.,Ye, H.,Lichtenstein, M.A.,Andries, K.,Pauwels, R.,De Bethune, M.P.,Boyer, P.L.,Clark, P.,Hughes, S.H.,Janssen, P.A.,Arnold, E.
      (2004) J.Med.Chem. 47: 2550
    • Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance.
      Huang, H.,Chopra, R.,Verdine, G.L.,Harrison, S.C.
      (1998) Science 282: 1669
    • High resolution structures of HIV-1 RT from four RT-inhibitor complexes.
      Ren, J.,Esnouf, R.,Garman, E.,Somers, D.,Ross, C.,Kirby, I.,Keeling, J.,Darby, G.,Jones, Y.,Stuart, D.
      (1995) Nat.Struct.Mol.Biol. 2: 293
    • Structural basis of HIV-1 resistance to AZT by excision.
      Tu, X.,Das, K.,Han, Q.,Bauman, J.D.,Clark, A.D.,Hou, X.,Frenkel, Y.V.,Gaffney, B.L.,Jones, R.A.,Boyer, P.L.,Hughes, S.H.,Sarafianos, S.G.,Arnold, E.
      (2010) Nat.Struct.Mol.Biol. 17: 1202
    • Structural basis for the role of the K65R mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance.
      Das, K.,Bandwar, R.P.,White, K.L.,Feng, J.Y.,Sarafianos, S.G.,Tuske, S.,Tu, X.,Clark, A.D.,Boyer, P.L.,Hou, X.,Gaffney, B.L.,Jones, R.A.,Miller, M.D.,Hughes, S.H.,Arnold, E.
      (2009) J.Biol.Chem. 284: 35092
    • High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations.
      Das, K.,Bauman, J.D.,Clark, A.D.,Frenkel, Y.V.,Lewi, P.J.,Shatkin, A.J.,Hughes, S.H.,Arnold, E.
      (2008) Proc.Natl.Acad.Sci.USA 105: 1466


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 Reverse Transcriptase P66 subunit
A, C
556Human immunodeficiency virus type 1 group M subtype BMutation(s): 3 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 Reverse Transcriptase P51 subunit
B, D
428Human immunodeficiency virus type 1 group M subtype BMutation(s): 1 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')T,E27N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')P,F21N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NVP
Query on NVP

Download SDF File 
Download CCD File 
A, C
11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE
NON-NUCLEOSIDE RT INHIBITOR NEVIRAPINE
C15 H14 N4 O
NQDJXKOVJZTUJA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ATM
Query on ATM
F, P
DNA LINKINGC10 H14 N5 O7 PDT
MRG
Query on MRG
F, P
DNA LINKINGC13 H20 N5 O7 P SDG
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NEVIC50: 2.6 - 23000 nM (98) BINDINGDB
NEVKi: 400 - 36000 nM (98) BINDINGDB
NEVEC50: 20 - >7500 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8503 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.251 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 89.822α = 90.00
b = 132.052β = 100.84
c = 142.732γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
ADSCdata collection
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2012-02-15
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description