3UEO

Crystal structure of TopBP1 BRCT4/5 domains in complex with a phospho-peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural insights into recognition of MDC1 by TopBP1 in DNA replication checkpoint control.

Leung, C.C., Sun, L., Gong, Z., Burkat, M., Edwards, R., Assmus, M., Chen, J., Glover, J.N.

(2013) Structure 21: 1450-1459

  • DOI: 10.1016/j.str.2013.06.015
  • Primary Citation of Related Structures:  
    3UEN, 3UEO

  • PubMed Abstract: 

    • Activation of the DNA replication checkpoint by the ATR kinase requires protein interactions mediated by the ATR-activating protein, TopBP1. Accumulation of TopBP1 at stalled replication forks requires the interaction of TopBP1 BRCT5 with the phosphorylated SDT repeats of the adaptor protein MDC1 ...

    Activation of the DNA replication checkpoint by the ATR kinase requires protein interactions mediated by the ATR-activating protein, TopBP1. Accumulation of TopBP1 at stalled replication forks requires the interaction of TopBP1 BRCT5 with the phosphorylated SDT repeats of the adaptor protein MDC1. Here, we present the X-ray crystal structures of the tandem BRCT4/5 domains of TopBP1 free and in complex with a MDC1 consensus pSDpT phosphopeptide. TopBP1 BRCT4/5 adopts a variant BRCT-BRCT packing interface and recognizes its target peptide in a manner distinct from that observed in previous tandem BRCT- peptide structures. The phosphate-binding pocket and positively charged residues in a variant loop in BRCT5 present an extended binding surface for the negatively charged MDC1 phosphopeptide. Mutations in this surface reduce binding affinity and recruitment of TopBP1 to γH2AX foci in cells. These studies reveal a different mode of phosphopeptide binding by BRCT domains in the DNA damage response.

    Organizational Affiliation: 

    Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 2-binding protein 1A, B, C, D203Homo sapiensMutation(s): 0 
Gene Names: KIAA0259, TOPBP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92547 (Homo sapiens)
Explore Q92547 
Go to UniProtKB:  Q92547
PHAROS:  Q92547
GTEx:  ENSG00000163781
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
phospho-peptideE, F12N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q14676 (Homo sapiens)
Explore Q14676 
Go to UniProtKB:  Q14676
PHAROS:  Q14676
GTEx:  ENSG00000137337
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		E, FL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO		E, FL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.81α = 102.05
b = 59.1β = 98.04
c = 78.31γ = 114.34
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2014-03-26
    Changes: Database references