4BU1 | pdb_00004bu1

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.288 (Depositor), 0.247 (DCC)
R-Value Work:
0.237 (Depositor)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

National Institute of Biological Sciences, 7 Science Park Road, ZGC Life Science Park, Beijing 102206, China.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32372
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P87074
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain U [auth C] SDF format, chain S [auth B] SDF format, chain P [auth B] SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth C] MOL2 format, chain S [auth B] MOL2 format, chain P [auth B] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth C] mmCIF format, chain S [auth B] mmCIF format, chain P [auth B] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A] I [auth A] M [auth B] N [auth B] O [auth B] 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		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on 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 (Depositor), 0.247 (DCC)
R-Value Work: 0.237 (Depositor)
R-Value Observed: 0.240 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-10-09

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.2: 2024-11-06
Changes: Structure summary