Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 27.84 kDa 
• Atom Count: 1961 
• Residue Count: 228 
• Unique protein chains: 2

3AL3

Crystal Structure of TopBP1 BRCT7/8-BACH1 peptide complex

• DOI: 10.2210/pdb3AL3/pdb

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


• Deposited: 2010-07-22 Released: 2010-12-01 
• Deposition Author(s): Leung, C.C., Glover, J.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.236 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Literature

Molecular basis of BACH1/FANCJ recognition by TopBP1 in DNA replication checkpoint control

Leung, C.C., Gong, Z., Chen, J., Glover, J.N.

(2011) J Biol Chem 286: 4292-4301

• PubMed: 21127055 
• DOI: 10.1074/jbc.M110.189555
• Primary Citation of Related Structures:  
  3AL2, 3AL3


• PubMed Abstract: 
  

The diverse roles of TopBP1 in DNA replication and checkpoint signaling are associated with the scaffolding ability of TopBP1 to initiate various protein-protein interactions. The recognition of the BACH1/FANCJ helicase by TopBP1 is critical for the activation of the DNA replication checkpoint at stalled replication forks and is facilitated by the C-terminal tandem BRCT7/8 domains of TopBP1 and a phosphorylated Thr(1133) binding motif in BACH1. Here we provide the structural basis for this interaction through analysis of the x-ray crystal structures of TopBP1 BRCT7/8 both free and in complex with a BACH1 phospho-peptide. In contrast to canonical BRCT-phospho-peptide recognition, TopBP1 BRCT7/8 undergoes a dramatic conformational change upon BACH1 binding such that the two BRCT repeats pivot about the central BRCT-BRCT interface to provide an extensive and deep peptide-binding cleft. Additionally, we provide the first structural mechanism for Thr(P) recognition among BRCT domains. Together with systematic mutagenesis studies, we highlight the role of key contacts in governing the unique specificity of the TopBP1-BACH1 interaction.

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Organizational Affiliation: 

Department of Biochemistry, School of Molecular and Systems Medicine, 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	235	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
Peptide of Fanconi anemia group J protein	B	10	N/A	Mutation(s): 0
Find proteins for Q9BX63 (Homo sapiens) Explore Q9BX63  Go to UniProtKB:  Q9BX63
NIH Common Fund Data Resources
PHAROS:  Q9BX63 GTEx:  ENSG00000136492

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	A	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.236 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.069	α = 90
b = 78.069	β = 90
c = 136.766	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-22 
• Released Date: 2010-12-01 
Deposition Author(s): Leung, C.C., Glover, J.N.

Revision History 

• Version 1.0: 2010-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-30
  Changes: Database references
• Version 1.3: 2017-10-11
  Changes: Refinement description