3PC8

X-ray crystal structure of the heterodimeric complex of XRCC1 and DNA ligase III-alpha BRCT domains.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structural basis for partitioning of the XRCC1/DNA ligase III-{alpha} BRCT-mediated dimer complexes.

Cuneo, M.J.Gabel, S.A.Krahn, J.M.Ricker, M.A.London, R.E.

(2011) Nucleic Acids Res. 39: 7816-7827

  • DOI: 10.1093/nar/gkr419
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ultimate step common to almost all DNA repair pathways is the ligation of the nicked intermediate to form contiguous double-stranded DNA. In the mammalian nucleotide and base excision repair pathways, the ligation step is carried out by ligase II ...

    The ultimate step common to almost all DNA repair pathways is the ligation of the nicked intermediate to form contiguous double-stranded DNA. In the mammalian nucleotide and base excision repair pathways, the ligation step is carried out by ligase III-α. For efficient ligation, ligase III-α is constitutively bound to the scaffolding protein XRCC1 through interactions between the C-terminal BRCT domains of each protein. Although structural data for the individual domains has been available, no structure of the complex has been determined and several alternative proposals for this interaction have been advanced. Interpretation of the models is complicated by the formation of homodimers that, depending on the model, may either contribute to, or compete with heterodimer formation. We report here the structures of both homodimer complexes as well as the heterodimer complex. Structural characterization of the heterodimer formed from a longer XRCC1 BRCT domain construct, including residues comprising the interdomain linker region, revealed an expanded heterodimer interface with the ligase III-α BRCT domain. This enhanced linker-mediated binding interface plays a significant role in the determination of heterodimer/homodimer selectivity. These data provide fundamental insights into the structural basis of BRCT-mediated dimerization, and resolve questions related to the organization of this important repair complex.


    Organizational Affiliation

    National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA repair protein XRCC1
A, B
98Mus musculusMutation(s): 2 
Gene Names: Xrcc1 (Xrcc-1)
Find proteins for Q60596 (Mus musculus)
Go to UniProtKB:  Q60596
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA ligase 3
C, D
88Homo sapiensMutation(s): 1 
Gene Names: LIG3
EC: 6.5.1.1
Find proteins for P49916 (Homo sapiens)
Go to Gene View: LIG3
Go to UniProtKB:  P49916
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
D
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 66.320α = 90.00
b = 163.480β = 90.00
c = 36.740γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
StructureStudiodata collection
XSCALEdata processing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-02
    Type: Database references