3OS2

PFV target capture complex (TCC) at 3.32 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

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:  
    3OS0, 3OS1, 3OS2

  • 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 DNA ends ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IntegraseA, B395Human spumaretrovirusMutation(s): 0 
Gene Names: pol
EC: 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.4 (UniProt), 3.4.23 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P14350 (Human spumaretrovirus)
Explore P14350 
Go to UniProtKB:  P14350
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    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
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')D17N/A
      Protein Feature View
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      • Reference Sequence
      Find similar nucleic acids by:  (by identity cutoff)  |  Structure
      Entity ID: 4
      MoleculeChainsLengthOrganismImage
      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')E [auth T]30N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SO4
      Query on SO4

      Download Ideal Coordinates CCD File 
      G [auth B]SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      F [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.32 Å
      • R-Value Free: 0.260 
      • R-Value Work: 0.224 
      • R-Value Observed: 0.225 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 160.951α = 90
      b = 160.951β = 90
      c = 127.933γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      XDSdata reduction
      SCALAdata scaling

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

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