1T03

HIV-1 reverse transcriptase crosslinked to tenofovir terminated template-primer (complex P)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure 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 BMutations: S280C, C258Q
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 BMutations: S280C
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
monoclonal antibody light chain
L
211N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
monoclonal antibody heavy chain
H
225N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
Synthetic oligonucleotide templateT27N/A
Entity ID: 2
MoleculeChainsLengthOrganism
Synthetic oligonucleotide primerP21N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
MRG
Query on MRG
P
DNA LINKINGC13 H20 N5 O7 P SDG
TFO
Query on TFO
P
DNA LINKINGC9 H14 N5 O4 PDA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.256 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 166.780α = 90.00
b = 166.780β = 90.00
c = 221.130γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction

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: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance