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 

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.USA 107: 20057-20062

  • DOI: 10.1073/pnas.1010246107
  • Primary Citation of Related Structures:  3OYA, 3OYB, 3OYC, 3OYD, 3OYE, 3OYF, 3OYG, 3OYH, 3OYI, 3OYJ, 3OYK, 3OYL, 3OYN
  • Also Cited By: 3OY9, 3OYA

  • 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 prot ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PFV integrase
A, B
395Human spumaretrovirusGene Names: pol
EC: 3.1.26.4, 3.1.-.-, 2.7.7.49, 2.7.7.7, 2.7.7.-, 3.4.23.-
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*A)-3')D17N/A
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
HEZ
Query on HEZ

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B
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

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Download CCD File 
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 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 158.050α = 90.00
b = 158.050β = 90.00
c = 122.160γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
ADSCdata collection
PHASERphasing

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