3O4Q

Crystal structure of the Rous Associated Virus Integrase catalytic domain A182T in citrate buffer pH 6.2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A crystal structure of the catalytic core domain of an avian sarcoma and leukemia virus integrase suggests an alternate dimeric assembly.

Ballandras, A.Moreau, K.Robert, X.Confort, M.P.Merceron, R.Haser, R.Ronfort, C.Gouet, P.

(2011) Plos One 6: e23032-e23032

  • DOI: 10.1371/journal.pone.0023032
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Integrase (IN) is an important therapeutic target in the search for anti-Human Immunodeficiency Virus (HIV) inhibitors. This enzyme is composed of three domains and is hard to crystallize in its full form. First structural results on IN were obtained ...

    Integrase (IN) is an important therapeutic target in the search for anti-Human Immunodeficiency Virus (HIV) inhibitors. This enzyme is composed of three domains and is hard to crystallize in its full form. First structural results on IN were obtained on the catalytic core domain (CCD) of the avian Rous and Sarcoma Virus strain Schmidt-Ruppin A (RSV-A) and on the CCD of HIV-1 IN. A ribonuclease-H like motif was revealed as well as a dimeric interface stabilized by two pairs of α-helices (α1/α5, α5/α1). These structural features have been validated in other structures of IN CCDs. We have determined the crystal structure of the Rous-associated virus type-1 (RAV-1) IN CCD to 1.8 Å resolution. RAV-1 IN shows a standard activity for integration and its CCD differs in sequence from that of RSV-A by a single accessible residue in position 182 (substitution A182T). Surprisingly, the CCD of RAV-1 IN associates itself with an unexpected dimeric interface characterized by three pairs of α-helices (α3/α5, α1/α1, α5/α3). A182 is not involved in this novel interface, which results from a rigid body rearrangement of the protein at its α1, α3, α5 surface. A new basic groove that is suitable for single-stranded nucleic acid binding is observed at the surface of the dimer. We have subsequently determined the structure of the mutant A182T of RAV-1 IN CCD and obtained a RSV-A IN CCD-like structure with two pairs of buried α-helices at the interface. Our results suggest that the CCD of avian INs can dimerize in more than one state. Such flexibility can further explain the multifunctionality of retroviral INs, which beside integration of dsDNA are implicated in different steps of the retroviral cycle in presence of viral ssRNA.


    Organizational Affiliation

    Biocristallographie et Biologie Structurale des Cibles Thérapeutiques, Institut de Biologie et Chimie des Protéines, UMR 5086 BMSSI-Centre National de la Recherche Scientifique/Université de Lyon, Lyon, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
integrase
A
150Rous sarcoma virus (strain Schmidt-Ruppin B)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for O92956 (Rous sarcoma virus (strain Schmidt-Ruppin B))
Go to UniProtKB:  O92956
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCY
Query on OCY
A
L-PEPTIDE LINKINGC5 H11 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.164 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 65.490α = 90.00
b = 65.490β = 90.00
c = 79.160γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
REFMACphasing
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2012-01-11
    Type: Database references