3L2V

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with manganese and MK0518 (Raltegravir)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

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This is version 1.1 of the entry. See complete history


Literature

Retroviral intasome assembly and inhibition of DNA strand transfer

Hare, S.Gupta, S.S.Valkov, E.Engelman, A.Cherepanov, P.

(2010) Nature 464: 232-236

  • DOI: 10.1038/nature08784
  • Primary Citation of Related Structures:  
    3L2Q, 3L2R, 3L2U, 3L2V, 3L2W, 3OY9

  • PubMed Abstract: 
  • Integrase is an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The structure of full-length retroviral integrase, either separately or in complex with DNA, has been lacking. Furthermore, although clinically useful inhibitors of HIV integrase have been developed, their mechanism of action remains speculative ...

    Integrase is an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The structure of full-length retroviral integrase, either separately or in complex with DNA, has been lacking. Furthermore, although clinically useful inhibitors of HIV integrase have been developed, their mechanism of action remains speculative. Here we present a crystal structure of full-length integrase from the prototype foamy virus in complex with its cognate DNA. The structure shows the organization of the retroviral intasome comprising an integrase tetramer tightly associated with a pair of viral DNA ends. All three canonical integrase structural domains are involved in extensive protein-DNA and protein-protein interactions. The binding of strand-transfer inhibitors displaces the reactive viral DNA end from the active site, disarming the viral nucleoprotein complex. Our findings define the structural basis of retroviral DNA integration, and will allow modelling of the HIV-1 intasome to aid in the development of antiretroviral drugs.


    Organizational Affiliation

    Division of Medicine, 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): 2 
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
    5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*TP*GP*TP*A)-3'C19N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*AP*CP*AP*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
      Small Molecules
      Ligands 5 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      RLT (Subject of Investigation/LOI)
      Query on RLT

      Download Ideal Coordinates CCD File 
      I [auth A]N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide
      C20 H21 F N6 O5
      CZFFBEXEKNGXKS-UHFFFAOYSA-N
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      J [auth A], K [auth A], L [auth A], M [auth A]GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      E [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      MN
      Query on MN

      Download Ideal Coordinates CCD File 
      F [auth A], G [auth A], N [auth B]MANGANESE (II) ION
      Mn
      WAEMQWOKJMHJLA-UHFFFAOYSA-N
       Ligand Interaction
      NH4
      Query on NH4

      Download Ideal Coordinates CCD File 
      H [auth A]AMMONIUM ION
      H4 N
      QGZKDVFQNNGYKY-UHFFFAOYSA-O
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.20 Å
      • R-Value Free: 0.232 
      • R-Value Work: 0.205 
      • R-Value Observed: 0.206 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 158.65α = 90
      b = 158.65β = 90
      c = 125.23γ = 90
      Software Package:
      Software NamePurpose
      MOSFLMdata reduction
      SCALAdata scaling
      REFMACrefinement
      PDB_EXTRACTdata extraction
      ADSCdata collection
      PHASERphasing

      Structure Validation

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      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2010-02-09
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance