3OYM

Crystal structure of the PFV N224H mutant intasome bound to manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance.

Hare, S.Vos, A.M.Clayton, R.F.Thuring, J.W.Cummings, M.D.Cherepanov, P.

(2010) Proc Natl Acad Sci U S A 107: 20057-20062

  • DOI: 10.1073/pnas.1010246107
  • Primary Citation of Related Structures:  
    3OYM, 3OYN, 3OYE, 3OYF, 3OYG, 3OYH, 3OYI, 3OYJ, 3OYK, 3OYL

  • PubMed Abstract: 
  • The development of HIV integrase (IN) strand transfer inhibitors (INSTIs) and our understanding of viral resistance to these molecules have been hampered by a paucity of available structural data. We recently reported cocrystal structures of the prototype foamy virus (PFV) intasome with raltegravir and elvitegravir, establishing the general INSTI binding mode ...

    The development of HIV integrase (IN) strand transfer inhibitors (INSTIs) and our understanding of viral resistance to these molecules have been hampered by a paucity of available structural data. We recently reported cocrystal structures of the prototype foamy virus (PFV) intasome with raltegravir and elvitegravir, establishing the general INSTI binding mode. We now present an expanded set of cocrystal structures containing PFV intasomes complexed with first- and second-generation INSTIs at resolutions of up to 2.5 Å. Importantly, the improved resolution allowed us to refine the complete coordination spheres of the catalytic metal cations within the INSTI-bound intasome active site. We show that like the Q148H/G140S and N155H HIV-1 IN variants, the analogous S217H and N224H PFV INs display reduced sensitivity to raltegravir in vitro. Crystal structures of the mutant PFV intasomes in INSTI-free and -bound forms revealed that the amino acid substitutions necessitate considerable conformational rearrangements within the IN active site to accommodate an INSTI, thus explaining their adverse effects on raltegravir antiviral activity. Furthermore, our structures predict physical proximity and an interaction between HIV-1 IN mutant residues His148 and Ser/Ala140, rationalizing the coevolution of Q148H and G140S/A mutations in drug-resistant viral strains.


    Organizational Affiliation

    Division of Infectious Diseases, Imperial College London, London W2 1PG, United Kingdom.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PFV integraseA, B395Human spumaretrovirusMutation(s): 3 
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)
Find proteins for P14350 (Human spumaretrovirus)
Explore P14350 
Go to UniProtKB:  P14350
Protein Feature View
Expand
  • 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
    • 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
      Small Molecules
      Ligands 6 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      HEZ
      Query on HEZ

      Download Ideal Coordinates CCD File 
      Q [auth B]HEXANE-1,6-DIOL
      C6 H14 O2
      XXMIOPMDWAUFGU-UHFFFAOYSA-N
       Ligand Interaction
      SO4
      Query on SO4

      Download Ideal Coordinates CCD File 
      G [auth A], J [auth A], P [auth B]SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      H [auth A], K [auth A], M [auth B], O [auth B], R [auth C]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], L [auth B], N [auth B]MANGANESE (II) ION
      Mn
      WAEMQWOKJMHJLA-UHFFFAOYSA-N
       Ligand Interaction
      NH4
      Query on NH4

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

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.02 Å
      • R-Value Free: 0.228 
      • R-Value Work: 0.197 
      • R-Value Observed: 0.199 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 158.05α = 90
      b = 158.05β = 90
      c = 122.16γ = 90
      Software Package:
      Software NamePurpose
      MOSFLMdata reduction
      SCALAdata scaling
      PHASERphasing
      REFMACrefinement
      PDB_EXTRACTdata extraction
      ADSCdata collection

      Structure Validation

      View Full Validation Report



      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