1N6Q

HIV-1 Reverse Transcriptase Crosslinked to pre-translocation AZTMP-terminated DNA (complex N)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of HIV-1 Reverse Transcriptase with Pre- and Post-translocation AZTMP-terminated DNA

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

(2002) EMBO J 21: 6614-6624

  • DOI: 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) ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Reverse TranscriptaseC [auth A]558Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: POL
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (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))
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Go to UniProtKB:  P03366
Entity Groups  
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UniProt GroupP03366
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Reverse TranscriptaseD [auth B]430Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: POL
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (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))
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Go to UniProtKB:  P03366
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UniProt GroupP03366
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal Antibody (Light Chain)E [auth L]211Mus musculusMutation(s): 0 
UniProt
Find proteins for I6L991 (Mus musculus)
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Go to UniProtKB:  I6L991
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UniProt GroupI6L991
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal Antibody (Heavy Chain)F [auth H]225Mus musculusMutation(s): 0 
Gene Names: Ighg1Igh-4
UniProt
Find proteins for P01868 (Mus musculus)
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UniProt GroupP01868
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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*AP*T*GP*CP*AP*TP*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
MoleculeChainsLengthOrganismImage
5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*AP*(ATM))-3'B [auth P]22N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.247 
  • Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.35α = 90
b = 166.35β = 90
c = 220.96γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-14
    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