1N5Y

HIV-1 Reverse Transcriptase Crosslinked to Post-Translocation AZTMP-Terminated DNA (Complex P)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of HIV-1 Reverse Transcriptase with Pre-Translocation and Post-Translocation AZTMP-Terminated DNA

Sarafianos, S.G.Clark Jr., A.D.Das, K.Tuske, S.Birktoft, J.J.Ilankumaran, P.Ramesha, A.R.Sayer, J.M.Jerina, D.M.Boyer, P.L.Hughes, S.H.Arnold, E.

(2002) EMBO J 21: 6614-6624

  • DOI: https://doi.org/10.1093/emboj/cdf637
  • Primary Citation of Related Structures:  
    1N5Y, 1N6Q

  • PubMed Abstract: 

    AZT (3'-azido-3'-deoxythymidine) resistance involves the enhanced excision of AZTMP from the end of the primer strand by HIV-1 reverse transcriptase. This reaction can occur when an AZTMP-terminated primer is bound at the nucleotide-binding site (pre-translocation complex N) but not at the 'priming' site (post-translocation complex P). We determined the crystal structures of N and P complexes at 3.0 and 3.1 A resolution. These structures provide insight into the structural basis of AZTMP excision and the mechanism of translocation. Docking of a dNTP in the P complex structure suggests steric crowding in forming a stable ternary complex that should increase the relative amount of the N complex, which is the substrate for excision. Structural differences between complexes N and P suggest that the conserved YMDD loop is involved in translocation, acting as a springboard that helps to propel the primer terminus from the N to the P site after dNMP incorporation.


  • Organizational Affiliation

    Center for Advanced Biotechnology and Medicine, 679 Hoes Lane, Piscataway, NJ 08854-5638, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
REVERSE TRANSCRIPTASEC [auth A]558Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: POL
EC: 2.7.7.49
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
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Go to UniProtKB:  P03366
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UniProt GroupP03366
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
REVERSE TRANSCRIPTASED [auth B]430Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: POL
EC: 2.7.7.49
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
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UniProt GroupP03366
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
monoclonal antibody (light chain)E [auth L]211Mus musculusMutation(s): 0 
UniProt
Find proteins for P01837 (Mus musculus)
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UniProt GroupP01837
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
monoclonal antibody (heavy chain)F [auth H]225Mus musculusMutation(s): 0 
UniProt
Find proteins for P01868 (Mus musculus)
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UniProt GroupP01868
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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*AP*TP*GP*C*TP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3'A [auth T]27N/A
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Entity ID: 2
MoleculeChains LengthOrganismImage
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'B [auth P]21N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.7α = 90
b = 166.7β = 90
c = 221.12γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-28
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-10-30
    Changes: Data collection, Structure summary