1T05

HIV-1 reverse transcriptase crosslinked to template-primer with tenofovir-diphosphate bound as the incoming nucleotide substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 469-474

  • DOI: 10.1038/nsmb760
  • Primary Citation of Related Structures:  
  • Also Cited By: 3JYT, 3JSM

  • PubMed Abstract: 
  • Tenofovir, also known as PMPA, R-9-(2-(phosphonomethoxypropyl)adenine, is a nucleotide reverse transcriptase (RT) inhibitor. We have determined the crystal structures of two related complexes of HIV-1 RT with template primer and tenofovir: (i) a tern ...

    Tenofovir, also known as PMPA, R-9-(2-(phosphonomethoxypropyl)adenine, is a nucleotide reverse transcriptase (RT) inhibitor. We have determined the crystal structures of two related complexes of HIV-1 RT with template primer and tenofovir: (i) a ternary complex at a resolution of 3.0 A of RT crosslinked to a dideoxy-terminated DNA with tenofovir-diphosphate bound as the incoming substrate; and (ii) a RT-DNA complex at a resolution of 3.1 A with tenofovir at the 3' primer terminus. The tenofovir nucleotide in the tenofovir-terminated structure seems to adopt multiple conformations. Some nucleoside reverse transcriptase inhibitors, including 3TC and AZT, have elements ('handles') that project beyond the corresponding elements on normal dNTPs (the 'substrate envelope'). HIV-1 RT resistance mechanisms to AZT and 3TC take advantage of these handles; tenofovir's structure lacks handles that could protrude through the substrate envelope to cause resistance.


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine and Rutgers University Department of Chemistry and Chemical Biology, 679 Hoes Lane, Piscataway, New Jersey 08854-5638, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
POL polyprotein
A
558Human immunodeficiency virus type 1 group M subtype BMutation(s): 2 
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
POL polyprotein
B
437Human immunodeficiency virus type 1 group M subtype BMutation(s): 1 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Entity ID: 1
MoleculeChainsLengthOrganism
oligonucleotide templateT27N/A
Entity ID: 2
MoleculeChainsLengthOrganism
oligonucleotide primerP21N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TNV
Query on TNV

Download SDF File 
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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
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: 0.292 
  • R-Value Work: 0.253 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 171.570α = 90.00
b = 171.570β = 90.00
c = 156.270γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance