4BU1

Crystal structure of Rad4 BRCT1,2 in complex with a Crb2 phosphopeptide

• PDB DOI: https://doi.org/10.2210/pdb4BU1/pdb

• Classification: REPLICATION
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-06-19 Released: 2013-10-09 
• Deposition Author(s): Qu, M., 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: 2.10 Å
• R-Value Free: 0.288 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 

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 of 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47.15 kDa 
• Atom Count: 3,613 
• Modelled Residue Count: 389 
• Deposited Residue Count: 400 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-M CHECKPOINT CONTROL PROTEIN RAD4	A, B	186	Schizosaccharomyces pombe	Mutation(s): 1
UniProt
Find proteins for P32372 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P32372  Go to UniProtKB:  P32372

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA REPAIR PROTEIN RHP9	C, D	14	Schizosaccharomyces pombe	Mutation(s): 0
UniProt
Find proteins for P87074 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P87074  Go to UniProtKB:  P87074

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	G [auth A], L [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PO4	E [auth A], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth A], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.288 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.439	α = 90
b = 76.844	β = 90
c = 92.136	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
CrystalClear	data reduction
DTSCALEAVERAGE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-09 
Deposition Author(s): Qu, M., 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