3V4I

Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and AZTTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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:  
    3V4I, 3V6D, 3V81

  • 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 NNRTIs is not clear ...

    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: 
    • 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
    • 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
    • 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 U S A 105: 1466
    • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 Reverse Transcriptase P66 subunitA, C556Human immunodeficiency virus type 1 BH10Mutation(s): 3 
Gene Names: gag-pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.4.23.16 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 Reverse Transcriptase P51 subunitB, D428Human immunodeficiency virus type 1 BH10Mutation(s): 1 
Gene Names: gag-pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.4.23.16 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
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')F [auth E], E [auth T]27N/A
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')H [auth F], G [auth P]21N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AZT (Subject of Investigation/LOI)
Query on AZT

Download Ideal Coordinates CCD File 
J [auth A], L [auth C]3'-AZIDO-3'-DEOXYTHYMIDINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
GLWHPRRGGYLLRV-XLPZGREQSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A], K [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
AZT BindingDB:  3V4I Ki: 91 (nM) from 1 assay(s)
IC50: min: 3, max: 2100 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.053α = 90
b = 132.647β = 98.12
c = 138.014γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2012-01-25
    Changes: Derived calculations
  • Version 1.2: 2012-02-15
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description