Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 101.1 kDa 
• Atom Count: 5,399 
• Modelled Residue Count: 588 
• Deposited Residue Count: 826 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 3OYA

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and raltegravir at 2.65 resolution

• PDB DOI:  https://doi.org/10.2210/pdb3OYA/pdb
• Entry: 3OYA supersedes: 3L2T
• NDB: NA0781

• Classification: RECOMBINATION,VIRAL PROTEIN/DNA
• Organism(s): Human spumaretrovirus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-09-23 Released: 2010-10-20 
• Deposition Author(s): Hare, S., Cherepanov, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.228 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 

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

• PubMed: 21030679 
• DOI: https://doi.org/10.1073/pnas.1010246107
• Primary Citation of Related Structures:  
  3OYA, 3OYB, 3OYC, 3OYD, 3OYE, 3OYF, 3OYG, 3OYH, 3OYI, 3OYJ, 3OYK, 3OYL, 3OYM, 3OYN


• 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. 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.

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Related Citations: 

• 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 --: --

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PFV integrase	A, B	395	Human spumaretrovirus	Mutation(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 ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')	C	19	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')	D	17	N/A

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RLT	M [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
SO4	F [auth A], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A], I [auth A], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	K [auth A], L [auth A], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NH4	J [auth A]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.228 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.755	α = 90
b = 159.755	β = 90
c = 124.139	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-20 
Deposition Author(s): Hare, S., Cherepanov, P.
• This entry supersedes: 3L2T

Revision History  

• Version 1.0: 2010-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance