4E7J

PFV integrase Target Capture Complex, Apo form (TCC-Apo), at 3.15 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1501 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

3'-Processing and strand transfer catalysed by retroviral integrase in crystallo.

Hare, S.Maertens, G.N.Cherepanov, P.

(2012) Embo J. 468: 326-329

  • DOI: 10.1038/emboj.2012.118
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Retroviral integrase (IN) is responsible for two consecutive reactions, which lead to insertion of a viral DNA copy into a host cell chromosome. Initially, the enzyme removes di- or trinucleotides from viral DNA ends to expose 3'-hydroxyls attached t ...

    Retroviral integrase (IN) is responsible for two consecutive reactions, which lead to insertion of a viral DNA copy into a host cell chromosome. Initially, the enzyme removes di- or trinucleotides from viral DNA ends to expose 3'-hydroxyls attached to the invariant CA dinucleotides (3'-processing reaction). Second, it inserts the processed 3'-viral DNA ends into host chromosomal DNA (strand transfer). Herein, we report a crystal structure of prototype foamy virus IN bound to viral DNA prior to 3'-processing. Furthermore, taking advantage of its dependence on divalent metal ion cofactors, we were able to freeze trap the viral enzyme in its ground states containing all the components necessary for 3'-processing or strand transfer. Our results shed light on the mechanics of retroviral DNA integration and explain why HIV IN strand transfer inhibitors are ineffective against the 3'-processing step of integration. The ground state structures moreover highlight a striking substrate mimicry utilized by the inhibitors in their binding to the IN active site and suggest ways to improve upon this clinically relevant class of small molecules.


    Related Citations: 
    • 3'-Processing and strand transfer calalysed by retroviral integrase in crystallo
      Maertens, G.N.,Hare, S.,Cherepanov, P.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Division of Infectious Diseases, Imperial College London, London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pro-Pol polyprotein
A, B
395Human spumaretrovirusMutation(s): 0 
Gene Names: pol
Find proteins for P14350 (Human spumaretrovirus)
Go to UniProtKB:  P14350
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')C19N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')D17N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*CP*GP*AP*GP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*CP*TP*CP*GP*GP*G)-3')T30N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1501 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.222 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 159.339α = 90.00
b = 159.339β = 90.00
c = 127.197γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-23
    Type: Initial release