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- PDB-2vxc: Structure of the Crb2-BRCT2 domain complex with phosphopeptide. -

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Basic information

Entry
Database: PDB / ID: 2vxc
TitleStructure of the Crb2-BRCT2 domain complex with phosphopeptide.
Components
  • DNA REPAIR PROTEIN RHP9
  • H2A1 PEPTIDE
KeywordsCELL CYCLE / BRCT / NUCLEUS / DNA DAMAGE / DNA REPLICATION INHIBITOR / PHOSPHOPROTEIN / CHECKPOINT SIGNALLING
Function / homology
Function and homology information


SUMOylation of transcription factors / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic DNA damage checkpoint signaling / chromatin-protein adaptor activity / mitotic DNA replication checkpoint signaling / regulation of double-strand break repair via homologous recombination / negative regulation of DNA replication / mitotic G2 DNA damage checkpoint signaling / methylated histone binding / DNA damage checkpoint signaling ...SUMOylation of transcription factors / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic DNA damage checkpoint signaling / chromatin-protein adaptor activity / mitotic DNA replication checkpoint signaling / regulation of double-strand break repair via homologous recombination / negative regulation of DNA replication / mitotic G2 DNA damage checkpoint signaling / methylated histone binding / DNA damage checkpoint signaling / site of double-strand break / histone binding / chromatin / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / : / : / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / : / : / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PRASEODYMIUM ION / DNA repair protein crb2
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKilkenny, M.L. / Roe, S.M. / Pearl, L.H.
CitationJournal: Genes Dev. / Year: 2008
Title: Structural and Functional Analysis of the Crb2-Brct2 Domain Reveals Distinct Roles in Checkpoint Signaling and DNA Damage Repair.
Authors: Kilkenny, M.L. / Dore, A. / Roe, S.M. / Nestoras, K. / Ho, J.C.Y. / Watts, F.Z. / Pearl, L.H.
History
DepositionJul 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA REPAIR PROTEIN RHP9
B: DNA REPAIR PROTEIN RHP9
C: H2A1 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1727
Polymers55,6093
Non-polymers5644
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-33.5 kcal/mol
Surface area24030 Å2
MethodPQS
Unit cell
Length a, b, c (Å)73.358, 140.415, 56.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 538:586 OR RESSEQ 592:698 OR RESSEQ 710:749 OR RESSEQ 759:778 )
211CHAIN B AND (RESSEQ 538:586 OR RESSEQ 592:698 OR RESSEQ 710:749 OR RESSEQ 759:778 )

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Components

#1: Protein DNA REPAIR PROTEIN RHP9 / RAD9 HOMOLOG / CHECKPOINT PROTEIN CRB2


Mass: 27526.613 Da / Num. of mol.: 2 / Fragment: BRCT DOMAIN, RESIDUES 537-778
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Strain: SP.011 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): PRSETB / References: UniProt: P87074
#2: Protein/peptide H2A1 PEPTIDE


Mass: 555.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PHOSPHOSERINE AT C139 / Source: (synth.) HOMO SAPIENS (human)
#3: Chemical
ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.49 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: CRB2-BRCT2 (3.5MG/ML IN 0.05M TRIS-HCL PH7.0, 0.6M NACL, 5MM DTT) WAS MIXED WITH AN EQUAL VOLUME OF PEPTIDE (0.05M TRIS-HCL PH7.0, 0.1M NACL, 5MM DTT), TO GIVE A 1:30 MOLAR RATIO OF PROTEIN: ...Details: CRB2-BRCT2 (3.5MG/ML IN 0.05M TRIS-HCL PH7.0, 0.6M NACL, 5MM DTT) WAS MIXED WITH AN EQUAL VOLUME OF PEPTIDE (0.05M TRIS-HCL PH7.0, 0.1M NACL, 5MM DTT), TO GIVE A 1:30 MOLAR RATIO OF PROTEIN:PEPTIDE. CRB2-BRCT2/PEPTIDE (7MG/ML IN 0.05M TRIS-HCL PH7.0, 1M NACL, 5MM DTT) WERE CRYSTALLISED BY HANGING DROP VAPOUR DIFFUSION AT 20C. PLATECLUSTERS GREW FROM 2UL PROTEIN, 2UL WELL SOLUTION (0.1M NA-CACODYLATE PH6.5, 7.0% PEG8000 AND 0.2M CA-ACETATE) AND 0.5UL 0.1M PR(III) ACETATE.

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06
DetectorType: ADSC CCD / Detector: CCD / Date: May 31, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 3.1→70 Å / Num. obs: 11193 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 53.11 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.5
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN HOUSE STRUCTURE

Resolution: 3.1→65 Å / SU ML: 0.41 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 968 4.8 %
Rwork0.1952 --
obs0.1976 20371 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.99 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 57.77 Å2
Baniso -1Baniso -2Baniso -3
1--1.3932 Å20 Å20 Å2
2--4.1243 Å2-0 Å2
3----2.731 Å2
Refinement stepCycle: LAST / Resolution: 3.1→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3517 0 4 39 3560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073598
X-RAY DIFFRACTIONf_angle_d1.0474903
X-RAY DIFFRACTIONf_dihedral_angle_d16.8491257
X-RAY DIFFRACTIONf_chiral_restr0.07567
X-RAY DIFFRACTIONf_plane_restr0.005636
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1653X-RAY DIFFRACTIONPOSITIONAL
12B1653X-RAY DIFFRACTIONPOSITIONAL0.039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.26340.30441520.24752741X-RAY DIFFRACTION100
3.2634-3.46790.29631450.22042819X-RAY DIFFRACTION100
3.4679-3.73560.2721350.20492766X-RAY DIFFRACTION99
3.7356-4.11150.28051290.1682808X-RAY DIFFRACTION99
4.1115-4.70630.15741400.14412770X-RAY DIFFRACTION99
4.7063-5.92880.19441280.17212745X-RAY DIFFRACTION98
5.9288-65.03350.2441390.21892754X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9561-0.0849-0.02120.89510.32062.22930.0732-0.1587-0.19250.00050.0014-0.04210.4034-0.0434-0.00010.14360.0157-0.02990.1302-0.02930.2257-17.065919.2577-4.9341
20.78160.72860.53381.16220.05410.7944-0.14950.42-0.0142-0.45050.0768-0.0088-0.10270.352-0.00080.343-0.00670.08570.2918-0.01980.1527-1.153138.8413-21.0865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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