[English] 日本語
Yorodumi
- PDB-6hm5: Crystal structure of TOPBP1 BRCT0,1,2 in complex with a RAD9 phos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hm5
TitleCrystal structure of TOPBP1 BRCT0,1,2 in complex with a RAD9 phosphopeptide
Components
  • Cell cycle checkpoint control protein RAD9A
  • DNA topoisomerase II binding protein 1
KeywordsCELL CYCLE / BRCT domain phosphopeptide recognition
Function / homology
Function and homology information


HDR through Single Strand Annealing (SSA) / Processing of DNA double-strand break ends / broken chromosome clustering / checkpoint clamp complex / BRCA1-B complex / phosphorylation-dependent protein binding / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA replication checkpoint signaling / chromatin-protein adaptor activity ...HDR through Single Strand Annealing (SSA) / Processing of DNA double-strand break ends / broken chromosome clustering / checkpoint clamp complex / BRCA1-B complex / phosphorylation-dependent protein binding / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA replication checkpoint signaling / chromatin-protein adaptor activity / double-strand break repair via alternative nonhomologous end joining / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / HDR through Single Strand Annealing (SSA) / response to ionizing radiation / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / DNA replication initiation / Activation of ATR in response to replication stress / 3'-5' exonuclease activity / male germ cell nucleus / protein serine/threonine kinase activator activity / DNA damage checkpoint signaling / condensed nuclear chromosome / cellular response to ionizing radiation / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / PML body / SH3 domain binding / histone deacetylase binding / intrinsic apoptotic signaling pathway in response to DNA damage / actin cytoskeleton / site of double-strand break / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA repair / DNA damage response / protein kinase binding / enzyme binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Rad9 / Rad9 / : / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / : / Secretoglobin superfamily / Rad9/Ddc1 / twin BRCT domain / BRCT domain ...Rad9 / Rad9 / : / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / : / Secretoglobin superfamily / Rad9/Ddc1 / 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
DNA topoisomerase II binding protein 1 / Cell cycle checkpoint control protein RAD9A
Similarity search - Component
Biological speciesGallus gallus (chicken)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.33003812226 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 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA topoisomerase II binding protein 1
B: Cell cycle checkpoint control protein RAD9A


Theoretical massNumber of molelcules
Total (without water)34,3682
Polymers34,3682
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-9 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.050, 34.070, 66.670
Angle α, β, γ (deg.)90.000, 103.570, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein DNA topoisomerase II binding protein 1


Mass: 33156.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TOPBP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D5P3M9
#2: Protein/peptide Cell cycle checkpoint control protein RAD9A / hRAD9 / DNA repair exonuclease rad9 homolog A


Mass: 1212.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99638, exodeoxyribonuclease III
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM bicine/Trizma base pH 8.5, 300 mM diethyleneglycol, 300 mM triethyleneglycol, 300 mM tetraethyleneglycol, 300 mM pentaethyleneglycol, 10% w/v PEG 20000 and 20% v/v PEG MME 550

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91407 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91407 Å / Relative weight: 1
ReflectionResolution: 2.33→38.7 Å / Num. obs: 11242 / % possible obs: 98.97 % / Redundancy: 3 % / Biso Wilson estimate: 39.53 Å2 / Net I/σ(I): 9.72
Reflection shellResolution: 2.33→2.413 Å

-
Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.11.1_2575refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.33003812226→38.6991869814 Å / SU ML: 0.299558096022 / Cross valid method: FREE R-VALUE / σ(F): 1.34353251682 / Phase error: 24.5216819247
RfactorNum. reflection% reflection
Rfree0.241491216096 1125 10.0071161715 %
Rwork0.201270613267 --
obs0.205336955188 11242 99.0048436812 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.5979895974 Å2
Refinement stepCycle: LAST / Resolution: 2.33003812226→38.6991869814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 0 59 2115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002432412456822095
X-RAY DIFFRACTIONf_angle_d0.5163548218752828
X-RAY DIFFRACTIONf_chiral_restr0.0429592405889319
X-RAY DIFFRACTIONf_plane_restr0.00252518089053354
X-RAY DIFFRACTIONf_dihedral_angle_d14.28432706891276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.43610.3121051029941410.2495512939051274X-RAY DIFFRACTION99.298245614
2.4361-2.56450.2837552137271380.2251815852851239X-RAY DIFFRACTION99.7103548154
2.5645-2.72510.3151221586221400.2043453672941255X-RAY DIFFRACTION99.5717344754
2.7251-2.93540.2545216210951390.2045197999241253X-RAY DIFFRACTION99.7134670487
2.9354-3.23070.2626862089571410.2203216794011269X-RAY DIFFRACTION99.3657505285
3.2307-3.69790.237772618661410.1881560762011266X-RAY DIFFRACTION98.667601683
3.6979-4.65770.1800499144191380.180769686321253X-RAY DIFFRACTION98.1651376147
4.6577-38.70450.2479887854951470.2033022901331308X-RAY DIFFRACTION97.6510067114

+
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