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

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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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14350
Protein Feature View
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  • Reference Sequence

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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'C 19N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(*TP*AP*CP*AP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3'D 17N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RLT
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

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E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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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