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- PDB-6hm3: Crystal structure of Rad4 BRCT1,2 in complex with a Sld3 phosphop... -

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Basic information

Entry
Database: PDB / ID: 6hm3
TitleCrystal structure of Rad4 BRCT1,2 in complex with a Sld3 phosphopeptide
Components
  • DNA replication regulator sld3
  • S-M checkpoint control protein rad4
KeywordsCELL CYCLE / BRCT domain phosphopeptide recognition
Function / homology
Function and homology information


mitotic DNA damage checkpoint signaling / mitotic spindle pole body / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / mitotic DNA replication initiation / mitotic G2 DNA damage checkpoint signaling / DNA replication initiation / signaling adaptor activity / meiotic cell cycle / mitotic spindle ...mitotic DNA damage checkpoint signaling / mitotic spindle pole body / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / mitotic DNA replication initiation / mitotic G2 DNA damage checkpoint signaling / DNA replication initiation / signaling adaptor activity / meiotic cell cycle / mitotic spindle / site of double-strand break / chromatin / nucleus / cytosol
Similarity search - Function
DNA replication regulator Sld3, C-terminal / DNA replication regulator Sld3 / DNA replication regulator SLD3, STD domain / twin BRCT domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...DNA replication regulator Sld3, C-terminal / DNA replication regulator Sld3 / DNA replication regulator SLD3, STD domain / twin BRCT 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
S-M checkpoint control protein rad4 / DNA replication regulator sld3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77263620528 Å
AuthorsDay, M. / Rappas, M. / Oliver, A.W. / Pearl, L.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC302/A14532 United Kingdom
CitationJournal: Elife / Year: 2018
Title: BRCT domains of the DNA damage checkpoint proteins TOPBP1/Rad4 display distinct specificities for phosphopeptide ligands.
Authors: Day, M. / Rappas, M. / Ptasinska, K. / Boos, D. / Oliver, A.W. / Pearl, L.H.
History
DepositionSep 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-M checkpoint control protein rad4
B: DNA replication regulator sld3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9126
Polymers24,6482
Non-polymers2644
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-31 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.400, 59.170, 120.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein S-M checkpoint control protein rad4 / P74 / Protein cut5


Mass: 21236.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: rad4, cut5, SPAC23C4.18c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32372
#2: Protein/peptide DNA replication regulator sld3 / Meiotically up-regulated gene 175 protein


Mass: 3411.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09761
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / Details: Unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.77→42.2041207773 Å / Num. obs: 27589 / % possible obs: 98.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 26.18 Å2 / Net I/σ(I): 15.7
Reflection shellResolution: 1.77→1.82 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BMC

4bmc


Resolution: 1.77263620528→42.2041207773 Å / SU ML: 0.198039347248 / Cross valid method: FREE R-VALUE / σ(F): 1.3502924511 / Phase error: 24.8970812351
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.227838094068 1387 5.0346655051 %
Rwork0.191726600343 26162 -
obs0.193450598832 27549 97.9137048621 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.5473330333 Å2
Refinement stepCycle: LAST / Resolution: 1.77263620528→42.2041207773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 14 225 1898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006606119310461718
X-RAY DIFFRACTIONf_angle_d0.9044176059032338
X-RAY DIFFRACTIONf_chiral_restr0.0579433499164266
X-RAY DIFFRACTIONf_plane_restr0.00521200682112290
X-RAY DIFFRACTIONf_dihedral_angle_d11.25264949511390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7726-1.8360.3304588272721300.3017493371522614X-RAY DIFFRACTION99.4923857868
1.836-1.90950.2801775849561350.262768646542609X-RAY DIFFRACTION99.3123416576
1.9095-1.99640.3002956164241310.2335130313252602X-RAY DIFFRACTION99.2735197966
1.9964-2.10170.2451820027471250.2044944180182650X-RAY DIFFRACTION99.2489270386
2.1017-2.23330.2532572675861620.209478589882588X-RAY DIFFRACTION99.2779783394
2.2333-2.40570.2422218839841520.2015272639562624X-RAY DIFFRACTION99.2846924177
2.4057-2.64780.2504465927171560.205937548332615X-RAY DIFFRACTION98.5770188545
2.6478-3.03090.2280559598431500.196664834552582X-RAY DIFFRACTION96.7422096317
3.0309-3.81820.2116101432251380.1771895798182599X-RAY DIFFRACTION95.7997899895
3.8182-42.21610.1764555693961080.1618792050972679X-RAY DIFFRACTION92.6529255319

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