[English] 日本語
Yorodumi
- PDB-1l0b: Crystal Structure of rat Brca1 tandem-BRCT region -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1l0b
TitleCrystal Structure of rat Brca1 tandem-BRCT region
ComponentsBRCA1
KeywordsUNKNOWN FUNCTION / TANDEM-BRCT / THREE-HELIX BUNDLE
Function / homology
Function and homology information


HDR through Single Strand Annealing (SSA) / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / G2/M DNA damage checkpoint / Resolution of D-loop Structures through Holliday Junction Intermediates / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / HDR through Homologous Recombination (HRR) / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Metalloprotease DUBs ...HDR through Single Strand Annealing (SSA) / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / G2/M DNA damage checkpoint / Resolution of D-loop Structures through Holliday Junction Intermediates / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / HDR through Homologous Recombination (HRR) / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Metalloprotease DUBs / SUMOylation of DNA damage response and repair proteins / Regulation of TP53 Activity through Phosphorylation / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / sex-chromosome dosage compensation / negative regulation of intracellular estrogen receptor signaling pathway / random inactivation of X chromosome / response to genistein / nuclear ubiquitin ligase complex / chordate embryonic development / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / lateral element / protein K6-linked ubiquitination / XY body / mitotic G2/M transition checkpoint / centrosome cycle / RNA polymerase binding / postreplication repair / DNA repair complex / intracellular membraneless organelle / DNA-binding transcription activator activity / response to ionizing radiation / response to lipid / negative regulation of gene expression via chromosomal CpG island methylation / mitotic G2 DNA damage checkpoint signaling / negative regulation of reactive oxygen species metabolic process / positive regulation of vascular endothelial growth factor production / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / protein autoubiquitination / condensed chromosome / response to nutrient / male germ cell nucleus / positive regulation of DNA repair / condensed nuclear chromosome / cellular response to ionizing radiation / chromosome segregation / double-strand break repair via homologous recombination / negative regulation of cell growth / RING-type E3 ubiquitin transferase / positive regulation of protein import into nucleus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / fatty acid biosynthetic process / ubiquitin-protein transferase activity / p53 binding / cellular response to tumor necrosis factor / double-strand break repair / response to estradiol / chromosome / damaged DNA binding / transcription coactivator activity / transcription cis-regulatory region binding / regulation of cell cycle / protein ubiquitination / mitochondrial matrix / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. ...Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Breast cancer type 1 susceptibility protein homolog
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsJoo, W.S. / Jeffrey, P.D. / Cantor, S.B. / Finnin, M.S. / Livingston, D.M. / Pavletich, N.P.
CitationJournal: Genes Dev. / Year: 2002
Title: Structure of the 53BP1 BRCT region bound to p53 and its comparison to the Brca1 BRCT structure.
Authors: Joo, W.S. / Jeffrey, P.D. / Cantor, S.B. / Finnin, M.S. / Livingston, D.M. / Pavletich, N.P.
History
DepositionFeb 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BRCA1


Theoretical massNumber of molelcules
Total (without water)26,1051
Polymers26,1051
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.512, 58.722, 65.327
Angle α, β, γ (deg.)90.00, 111.28, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein BRCA1


Mass: 26104.854 Da / Num. of mol.: 1 / Fragment: tandem-BRCT region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O54952
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris-hydrochloride, sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-HCl1reservoirpH8.5
2150 mM1reservoirNaCl
318 %(w/v)PEG80001reservoir
45 mMdithiothreitol1reservoir
575 mg/mlprotein1drop
610 mMsodium HEPES1droppH7.5
7150 mM1dropNaCl
85 mMdithiothreitol1drop

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
31031
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.928
SYNCHROTRONNSLS X9A21.051
SYNCHROTRONNSLS X9A31.051
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 13, 2001
MARRESEARCH2CCDApr 28, 2001
MARRESEARCH3CCDApr 28, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rh-coated SiSINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
3Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9281
21.0511
ReflectionResolution: 2.1→15 Å / Num. obs: 17223 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.1→2.18 Å
Reflection
*PLUS
% possible obs: 97 % / Num. measured all: 55198 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.457

-
Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→15 Å / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 0 177 1700
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection obs: 12529 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.203 / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.61
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Rfactor Rfree: 0.341 / Rfactor Rwork: 0.262 / Rfactor obs: 0.262

+
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