Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.23 kDa 
• Atom Count: 2334 
• Modelled Residue Count: 280 
• Deposited Residue Count: 298 
• Unique protein chains: 1

3OLC

Crystal structure of the N-terminal region of TopBP1

• DOI: 10.2210/pdb3OLC/pdb

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


• Deposited: 2010-08-25 Released: 2011-03-30 
• Deposition Author(s): Huo, Y.G., Bai, L., Xu, M., Jiang, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.258 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Crystal structure of the N-terminal region of human Topoisomerase II beta binding protein 1

Huo, Y.G., Bai, L., Xu, M., Jiang, T.

(2010) Biochem Biophys Res Commun 401: 401-405

• PubMed: 20858457 
• DOI: 10.1016/j.bbrc.2010.09.066
• Primary Citation of Related Structures:  
  3OLC


• PubMed Abstract: 
  

Human DNA Topoisomerase IIβ binding protein 1 (TopBP1) is a modulating protein that plays an essential role in the response to DNA damage. The N-terminal region of TopBP1, which contains predicted BRCA1-carboxy terminal (BRCT) domains 1 and 2, binds to Rad9, a component of the cell cycle checkpoint clamp Rad9-Hus1-Rad1 complex. Here, we report the crystal structure of the TopBP1N-terminal region (residues 1-290) at 2.4Å resolution. Interestingly, in addition to the predicted tandem BRCT1-2 repeats (residues 103-284), residues 7-98 form a previously unreported BRCT domain (here, BRCT0). In contrast to both BRCT1 and BRCT2, which possess the conventional phosphopeptide binding residues within a surface pocket, the corresponding pocket in BRCT0 is largely hydrophobic. Structural comparisons together with peptide binding studies indicate that the tandem BRCT1-2 domains are the binding region for phosphorylated Ser387 in Rad9.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2-binding protein 1	A [auth X]	298	Homo sapiens	Mutation(s): 0  Gene Names: TOPBP1, KIAA0259
UniProt & NIH Common Fund Data Resources
Find proteins for Q92547 (Homo sapiens) Explore Q92547  Go to UniProtKB:  Q92547
PHAROS:  Q92547 GTEx:  ENSG00000163781

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth X]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.258 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.73	α = 90
b = 115.73	β = 90
c = 115.73	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-25 
• Released Date: 2011-03-30 
Deposition Author(s): Huo, Y.G., Bai, L., Xu, M., Jiang, T.

Revision History  

• Version 1.0: 2011-03-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance