3JSM

K65R mutant HIV-1 reverse transcriptase cross-linked to DS-DNA and complexed with tenofovir-diphosphate as the incoming nucleotide substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 35092-35100

  • DOI: 10.1074/jbc.M109.022525
  • Primary Citation of Related Structures:  
  • Also Cited By: 5TXP, 5TXO, 5TXN, 5TXM, 5TXL, 4R5P, 4Q0B, 4PWD, 4PUO, 4PQU, 3V81, 3V6D, 3V4I

  • PubMed Abstract: 
  • K65R is a primary reverse transcriptase (RT) mutation selected in human immunodeficiency virus type 1-infected patients taking antiretroviral regimens containing tenofovir disoproxil fumarate or other nucleoside analog RT drugs. We determined the cry ...

    K65R is a primary reverse transcriptase (RT) mutation selected in human immunodeficiency virus type 1-infected patients taking antiretroviral regimens containing tenofovir disoproxil fumarate or other nucleoside analog RT drugs. We determined the crystal structures of K65R mutant RT cross-linked to double-stranded DNA and in complexes with tenofovir diphosphate (TFV-DP) or dATP. The crystals permit substitution of TFV-DP with dATP at the dNTP-binding site. The guanidinium planes of the arginines K65R and Arg(72) were stacked to form a molecular platform that restricts the conformational adaptability of both of the residues, which explains the negative effects of the K65R mutation on nucleotide incorporation and on excision. Furthermore, the guanidinium planes of K65R and Arg(72) were stacked in two different rotameric conformations in TFV-DP- and dATP-bound structures that may help explain how K65R RT discriminates the drug from substrates. These K65R-mediated effects on RT structure and function help us to visualize the complex interaction with other key nucleotide RT drug resistance mutations, such as M184V, L74V, and thymidine analog resistance mutations.


    Related Citations: 
    • Structures of HIV-1 RT-DNA Complexes Before and After Incorporation of the Anti-Aids Drug Tenofovir
      Tuske, S.,Sarafianos, S.G.,Clark Jr., A.D.,Ding, J.,Naeger, L.K.,White, K.L.,Miller, M.D.,Gibbs, C.S.,Boyer, P.L.,Clark, P.,Wang, G.,Gaffney, B.L.,Jones, R.A.,Jerina, D.M.,Hughes, S.H.,Arnold, E.
      (2004) Nat.Struct.Mol.Biol. 11: 469


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, New Jersey 08854, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
A
558Human 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: 4
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
B
437Human 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: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*A*TP*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')T27N/A
Entity ID: 2
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*(DDG))-3')P21N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
TNV
Query on TNV

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Download CCD File 
A
[2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYL-TRIPHOSPHATE
TENOFOVIR-DIPHOSPHATE
C9 H16 N5 O10 P3
IACQCQDWSIQSRP-ZCFIWIBFSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
DDG
Query on DDG
P
DNA LINKINGC10 H14 N5 O6 PDG
MRG
Query on MRG
P
DNA LINKINGC13 H20 N5 O7 P SDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.252 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 170.310α = 90.00
b = 170.310β = 90.00
c = 155.440γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
CNSphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-09-10 
  • Released Date: 2009-09-29 
  • Deposition Author(s): Das, K., Arnold, E.

Revision History 

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance