3OYE

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI Compound2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


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, 3OYA, 3OYB, 3OYC, 3OYD

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PFV 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
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  • 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
      Small Molecules
      Ligands 6 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZYY (Subject of Investigation/LOI)
      Query on ZYY

      Download Ideal Coordinates CCD File 
      N [auth A]N-[(6S)-2-(4-fluorobenzyl)-10-hydroxy-6-methyl-8-(1-methylethyl)-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazin-4-yl]-N-methylmethanesulfonamide
      C22 H26 F N5 O5 S
      ITPCGSTZGSTIFB-ZDUSSCGKSA-N
       Ligand Interaction
      SO4
      Query on SO4

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

      Download Ideal Coordinates CCD File 
      G [auth A], H [auth A], I [auth A], J [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
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      L [auth A], M [auth A], P [auth B]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      NH4
      Query on NH4

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

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.74 Å
      • R-Value Free: 0.234 
      • R-Value Work: 0.204 
      • R-Value Observed: 0.205 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 159.5α = 90
      b = 159.5β = 90
      c = 123.11γ = 90
      Software Package:
      Software NamePurpose
      MOSFLMdata reduction
      SCALAdata scaling
      PHASERphasing
      REFMACrefinement
      PDB_EXTRACTdata extraction
      ADSCdata collection

      Structure Validation

      View Full Validation Report



      Ligand Structure Quality Assessment  



      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