3OS1

PFV target capture complex (TCC) at 2.97 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The mechanism of retroviral integration from X-ray structures of its key intermediates

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

(2010) Nature 468: 326-329

  • DOI: 10.1038/nature09517
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • To establish productive infection, a retrovirus must insert a DNA replica of its genome into host cell chromosomal DNA. This process is operated by the intasome, a nucleoprotein complex composed of an integrase tetramer (IN) assembled on the viral DN ...

    To establish productive infection, a retrovirus must insert a DNA replica of its genome into host cell chromosomal DNA. This process is operated by the intasome, a nucleoprotein complex composed of an integrase tetramer (IN) assembled on the viral DNA ends. The intasome engages chromosomal DNA within a target capture complex to carry out strand transfer, irreversibly joining the viral and cellular DNA molecules. Although several intasome/transpososome structures from the DDE(D) recombinase superfamily have been reported, the mechanics of target DNA capture and strand transfer by these enzymes remained unclear. Here we report crystal structures of the intasome from prototype foamy virus in complex with target DNA, elucidating the pre-integration target DNA capture and post-catalytic strand transfer intermediates of the retroviral integration process. The cleft between IN dimers within the intasome accommodates chromosomal DNA in a severely bent conformation, allowing widely spaced IN active sites to access the scissile phosphodiester bonds. Our results resolve the structural basis for retroviral DNA integration and provide a framework for the design of INs with altered target sequences.


    Organizational Affiliation

    Division of Infectious Diseases, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrase
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*(2DA))-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 3 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

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Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2DA
Query on 2DA
D
DNA LINKINGC10 H14 N5 O5 PDA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.231 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 159.882α = 90.00
b = 159.882β = 90.00
c = 127.842γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance