4BMD | pdb_00004bmd

Crystal structure of S.pombe Rad4 BRCT3,4

• PDB DOI: https://doi.org/10.2210/pdb4BMD/pdb

• Classification: REPLICATION
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-05-07 Released: 2013-10-09 
• Deposition Author(s): Meng, Q., Rappas, M., Wardlaw, C.P., Garcia, V., Carr, A.M., Oliver, A.W., Du, L.L., Pearl, L.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.218 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.184 (Depositor) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Phosphorylation-Dependent Assembly and Coordination of the DNA Damage Checkpoint Apparatus by Rad4(Topbp1.).

Qu, M., Rappas, M., Wardlaw, C.P., Garcia, V., Ren, J.Y., Day, M., Carr, A.M., Oliver, A.W., Du, L.L., Pearl, L.H.

(2013) Mol Cell 51: 723

• PubMed: 24074952 
• DOI: https://doi.org/10.1016/j.molcel.2013.08.030
• Primary Citation Related Structures: 
  4BMC, 4BMD, 4BU0, 4BU1


• PubMed Abstract: 
  

  The BRCT-domain protein Rad4(TopBP1) facilitates activation of the DNA damage checkpoint in Schizosaccharomyces pombe by physically coupling the Rad9-Rad1-Hus1 clamp, the Rad3(ATR) -Rad26(ATRIP) kinase complex, and the Crb2(53BP1) mediator. We have now determined crystal structures of the BRCT repeats of Rad4(TopBP1), revealing a distinctive domain architecture, and characterized their phosphorylation-dependent interactions with Rad9 and Crb2(53BP1). We identify a cluster of phosphorylation sites in the N-terminal region of Crb2(53BP1) that mediate interaction with Rad4(TopBP1) and reveal a hierarchical phosphorylation mechanism in which phosphorylation of Crb2(53BP1) residues Thr215 and Thr235 promotes phosphorylation of the noncanonical Thr187 site by scaffolding cyclin-dependent kinase (CDK) recruitment. Finally, we show that the simultaneous interaction of a single Rad4(TopBP1) molecule with both Thr187 phosphorylation sites in a Crb2(53BP1) dimer is essential for establishing the DNA damage checkpoint.

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Organizational Affiliation: 
• National Institute of Biological Sciences, 7 Science Park Road, ZGC Life Science Park, Beijing 102206, China.
Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK.
MRC Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 23.97 kDa 
• Atom Count: 1,749 
• Modeled Residue Count: 188 
• Deposited Residue Count: 204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-M CHECKPOINT CONTROL PROTEIN RAD4	A	204	Schizosaccharomyces pombe	Mutation(s): 0
UniProt
Find proteins for P32372 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P32372  Go to UniProtKB:  P32372

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.218 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.184 (Depositor) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.03	α = 90
b = 93.03	β = 90
c = 75.39	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-09 
Deposition Author(s): Meng, Q., Rappas, M., Wardlaw, C.P., Garcia, V., Carr, A.M., Oliver, A.W., Du, L.L., Pearl, L.H.

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description