[English] 日本語
Yorodumi
- PDB-4bu1: Crystal structure of Rad4 BRCT1,2 in complex with a Crb2 phosphop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bu1
TitleCrystal structure of Rad4 BRCT1,2 in complex with a Crb2 phosphopeptide
Components
  • DNA REPAIR PROTEIN RHP9
  • S-M CHECKPOINT CONTROL PROTEIN RAD4
KeywordsREPLICATION / TOPBP1 / DNA DAMAGE CHECKPOINT
Function / homology
Function and homology information


SUMOylation of transcription factors / mitotic DNA damage checkpoint signaling / mitotic spindle pole body / chromatin-protein adaptor activity / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / regulation of double-strand break repair via homologous recombination / negative regulation of DNA replication / nuclear replication fork / mitotic G2 DNA damage checkpoint signaling ...SUMOylation of transcription factors / mitotic DNA damage checkpoint signaling / mitotic spindle pole body / chromatin-protein adaptor activity / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / regulation of double-strand break repair via homologous recombination / negative regulation of DNA replication / nuclear replication fork / mitotic G2 DNA damage checkpoint signaling / DNA replication initiation / signaling adaptor activity / methylated histone binding / DNA damage checkpoint signaling / mitotic spindle / site of double-strand break / histone binding / chromatin / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytosol
Similarity search - Function
DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / twin BRCT domain / : / : / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain ...DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor 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
PHOSPHATE ION / S-M checkpoint control protein rad4 / DNA repair protein crb2
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsQu, M. / Rappas, M. / Wardlaw, C.P. / Garcia, V. / Carr, A.M. / Oliver, A.W. / Du, L.L. / Pearl, L.H.
CitationJournal: Mol.Cell / Year: 2013
Title: Phosphorylation-Dependent Assembly and Coordination of the DNA Damage Checkpoint Apparatus by Rad4(Topbp1.).
Authors: 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.
History
DepositionJun 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-M CHECKPOINT CONTROL PROTEIN RAD4
B: S-M CHECKPOINT CONTROL PROTEIN RAD4
C: DNA REPAIR PROTEIN RHP9
D: DNA REPAIR PROTEIN RHP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,15021
Polymers45,6164
Non-polymers1,53317
Water6,359353
1
B: S-M CHECKPOINT CONTROL PROTEIN RAD4
D: DNA REPAIR PROTEIN RHP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,73013
Polymers22,8082
Non-polymers92211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-3.3 kcal/mol
Surface area10880 Å2
MethodPISA
2
A: S-M CHECKPOINT CONTROL PROTEIN RAD4
C: DNA REPAIR PROTEIN RHP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4208
Polymers22,8082
Non-polymers6126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-10 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.439, 76.844, 92.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein S-M CHECKPOINT CONTROL PROTEIN RAD4 / P74 / PROTEIN CUT5


Mass: 21236.457 Da / Num. of mol.: 2 / Fragment: BRCT1,2 DOMAINS, RESIDUES 1-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: P32372
#2: Protein/peptide DNA REPAIR PROTEIN RHP9 / / RAD9 HOMOLOG / CRB2


Mass: 1571.646 Da / Num. of mol.: 2 / Fragment: PHOSPHOPEPTIDE, RESIDUES 229-241 / Source method: obtained synthetically / Source: (synth.) SCHIZOSACCHAROMYCES POMBE (fission yeast) / References: UniProt: P87074

-
Non-polymers , 5 types, 370 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.56 % / Description: NONE
Crystal growDetails: 100 MM NAK PHOSPHATE, 200 MM NACL, 40% W/V PEG 200

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.1→59.01 Å / Num. obs: 27555 / % possible obs: 99.2 % / Redundancy: 4.61 % / Biso Wilson estimate: 31.72 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.39 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.8 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
CrystalClear2data reduction
DTSCALEAVERAGEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BMC

4bmc


Resolution: 2.1→25.54 Å / Cor.coef. Fo:Fc: 0.9386 / Cor.coef. Fo:Fc free: 0.9068 / SU R Cruickshank DPI: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.289 / SU Rfree Blow DPI: 0.227 / SU Rfree Cruickshank DPI: 0.219
RfactorNum. reflection% reflectionSelection details
Rfree0.2879 1388 5.04 %RANDOM
Rwork0.2372 ---
obs0.2397 27525 99.18 %-
Displacement parametersBiso mean: 35.15 Å2
Baniso -1Baniso -2Baniso -3
1-4.6106 Å20 Å20 Å2
2---12.2353 Å20 Å2
3---7.6247 Å2
Refine analyzeLuzzati coordinate error obs: 0.319 Å
Refinement stepCycle: LAST / Resolution: 2.1→25.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 0 98 353 3577
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013326HARMONIC2
X-RAY DIFFRACTIONt_angle_deg14484HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1534SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes466HARMONIC5
X-RAY DIFFRACTIONt_it3326HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion2.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion424SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4103SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3021 131 4.88 %
Rwork0.2338 2554 -
all0.2372 2685 -
obs--99.18 %
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)
12.0268-0.1844-1.23931.1599-0.38031.8155-0.05880.0692-0.1326-0.0039-0.0532-0.05730.2369-0.24790.1119-0.0737-0.0192-0.00850.0336-0.0196-0.08971.3324-25.46371.4235
21.42630.0402-1.02642.0761.65873.6687-0.0632-0.07610.03640.04650.03640.05830.14990.02110.0268-0.06390.0196-0.00110.00790.0383-0.0823-16.2567-20.277819.0499
31.4796-0.09080.74050.7729-0.65492.9634-0.030.1170.10710.06490.1029-0.0442-0.29420.0143-0.0729-0.03980.0173-0.00940.02740.0247-0.0528-16.9008-10.626416.2229
41.7282-0.1336-1.02270.8952-0.21151.7998-0.0498-0.0762-0.11150.0063-0.06840.06170.14630.02830.1182-0.06840.00530.00030.01170.0142-0.0812-6.2906-25.665244.4426
50.54650.39020.02072.8019-1.65780.5938-0.02260.0806-0.08450.0290.0041-0.06710.06940.0020.0185-0.0291-0.00850.01520.0697-0.0319-0.04459.2725-25.047931.9223
61.33860.54650.08320.6191-0.62295.6732-0.02290.03630.06190.00020.03440.0073-0.09120.0455-0.0116-0.0886-0.0079-0.0031-0.0085-0.0188-0.060512.4097-13.782427.4386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|4 - 88}
2X-RAY DIFFRACTION2{A|92 - 149}
3X-RAY DIFFRACTION3{A|150 - 185}
4X-RAY DIFFRACTION4{B|4 - 87}
5X-RAY DIFFRACTION5{B|88 - 117}
6X-RAY DIFFRACTION6{B|118 - 185}

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more