Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 91.98 kDa 
• Atom Count: 6132 
• Residue Count: 762 
• Unique protein chains: 2

3UEO

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

• DOI: 10.2210/pdb3UEO/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-10-31 Released: 2013-07-03 
• Deposition Author(s): Leung, C.C., Glover, J.N.M.

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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 

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

• PubMed: 23891287 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2-binding protein 1	A, B, C, D	203	Homo sapiens	Mutation(s): 0  Gene Names: KIAA0259, TOPBP1
Find proteins for Q92547 (Homo sapiens) Explore Q92547  Go to UniProtKB:  Q92547
NIH Common Fund Data Resources
PHAROS:  Q92547 GTEx:  ENSG00000163781

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
phospho-peptide	E, F	12	N/A	Mutation(s): 0
Find proteins for Q14676 (Homo sapiens) Explore Q14676  Go to UniProtKB:  Q14676
NIH Common Fund Data Resources
PHAROS:  Q14676 GTEx:  ENSG00000137337

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	E,F	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	E,F	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

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 = 58.81	α = 102.05
b = 59.1	β = 98.04
c = 78.31	γ = 114.34

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-31 
• Released Date: 2013-07-03 
Deposition Author(s): Leung, C.C., Glover, J.N.M.

Revision History 

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