Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.41 kDa 
• Atom Count: 971 
• Residue Count: 95 
• Unique protein chains: 1

3JVE

Crystal Structure of the Sixth BRCT Domain of TopBP1

• DOI: 10.2210/pdb3JVE/pdb

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


• Deposited: 2009-09-16 Released: 2010-01-19 
• Deposition Author(s): Leung, C.C., Kellogg, E., Baker, D., Glover, J.N.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.173 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 

Literature

Insights from the crystal structure of the sixth BRCT domain of topoisomerase IIbeta binding protein 1.

Leung, C.C., Kellogg, E., Kuhnert, A., Hanel, F., Baker, D., Glover, J.N.

(2010) Protein Sci 19: 162-167

• PubMed: 19937654 
• DOI: 10.1002/pro.290
• Primary Citation of Related Structures:  
  3JVE


• PubMed Abstract: 
  

Topoisomerase IIbeta binding protein 1 (TopBP1) is a major player in the DNA damage response and interacts with a number of protein partners via its eight BRCA1 carboxy-terminal (BRCT) domains. In particular, the sixth BRCT domain of TopBP1 has been implicated in binding to the phosphorylated transcription factor, E2F1, and poly(ADP-ribose) polymerase 1 (PARP-1), where the latter interaction is responsible for the poly(ADP-ribosyl)ation of TopBP1. To gain a better understanding of the nature of TopBP1 BRCT6 interactions, we solved the crystal structure of BRCT6 to 1.34 A. The crystal structure reveals a degenerate phospho-peptide binding pocket and lacks conserved hydrophobic residues involved in packing of tandem BRCT repeats, which, together with results from phospho-peptide binding studies, strongly suggest that TopBP1 BRCT6 independently does not function as a phospho-peptide binding domain. We further provide insight into poly(ADP-ribose) binding and sites of potential modification by PARP-1.

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2-binding protein 1	A	109	Homo sapiens	Mutation(s): 0  Gene Names: TOPBP1, KIAA0259
Find proteins for Q92547 (Homo sapiens) Explore Q92547  Go to UniProtKB:  Q92547
NIH Common Fund Data Resources
PHAROS:  Q92547 GTEx:  ENSG00000163781

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.173 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.767	α = 90
b = 51.824	β = 90
c = 62.086	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-09-16 
• Released Date: 2010-01-19 
Deposition Author(s): Leung, C.C., Kellogg, E., Baker, D., Glover, J.N.M.

Revision History 

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description