Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 36019.35 
• Atom Count: 2297 
• Residue Count: 287 
• Unique protein chains: 1

2XNH

Structure and function of the Rad9-binding region of the DNA damage checkpoint adaptor TopBP1

• DOI: 10.2210/pdb2XNH/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2010-08-02 Released: 2010-09-01 
• Deposition Author(s): Rappas, M., Oliver, A.W., Pearl, L.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.251 
• R-Value Work: 0.232 

Literature

Structure and Function of the Rad9-Binding Region of the DNA-Damage Checkpoint Adaptor Topbp1.

Rappas, M., Oliver, A.W., Pearl, L.H.

(2011) Nucleic Acids Res. 39: 313

• PubMed: 20724438 
• DOI: 10.1093/nar/gkq743
• Primary Citation of Related Structures:  
  2XNK


• PubMed Abstract: 
  

TopBP1 is a scaffold protein that coordinates activation of the DNA-damage-checkpoint response by coupling binding of the 9-1-1 checkpoint clamp at sites of ssDNA, to activation of the ATR-ATRIP checkpoint kinase complex. We have now determined the crystal structure of the N-terminal region of human TopBP1, revealing an unexpected triple-BRCT domain structure. The arrangement of the BRCT domains differs significantly from previously described tandem BRCT domain structures, and presents two distinct sites for binding phosphopeptides in the second and third BRCT domains. We show that the site in the second but not third BRCT domain in the N-terminus of TopBP1, provides specific interaction with a phosphorylated motif at pSer387 in Rad9, which can be generated by CK2.

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Organizational Affiliation: 

Cancer Research UK DNA Repair Enzyme Group, Section of Structural Biology, The Institute of Cancer Research, London, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA TOPOISOMERASE 2-BINDING PROTEIN 1	A	287	Homo sapiens	Mutation(s): 0  Gene Names: TOPBP1 (KIAA0259)
Find proteins for Q92547 (Homo sapiens) Go to Gene View: TOPBP1 Go to UniProtKB:  Q92547

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
IOD	A	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.251 
• R-Value Work: 0.232 
• Space Group: P 2₁ 3

Unit Cell:

Length (Å)	Angle (°)
a = 115.770	α = 90.00
b = 115.770	β = 90.00
c = 115.770	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
MOSFLM	data reduction
SHELX	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-02 
• Released Date: 2010-09-01 
• Deposition Author(s): Rappas, M., Oliver, A.W., Pearl, L.H.

Revision History 

• Version 1.0: 2010-09-01
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance