[English] 日本語
Yorodumi
- PDB-1jnx: Crystal structure of the BRCT repeat region from the breast cance... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jnx
TitleCrystal structure of the BRCT repeat region from the breast cancer associated protein, BRCA1
ComponentsBREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN
KeywordsGENE REGULATION / BRCT / CANCER / GENE EXPRESSION
Function / homology
Function and homology information


histone H2AK127 ubiquitin ligase activity / histone H2AK129 ubiquitin ligase activity / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / negative regulation of centriole replication / sex-chromosome dosage compensation ...histone H2AK127 ubiquitin ligase activity / histone H2AK129 ubiquitin ligase activity / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / negative regulation of centriole replication / sex-chromosome dosage compensation / negative regulation of intracellular estrogen receptor signaling pathway / random inactivation of X chromosome / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / ubiquitin-modified histone reader activity / chordate embryonic development / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / DNA strand resection involved in replication fork processing / homologous recombination / lateral element / protein K6-linked ubiquitination / Impaired BRCA2 binding to PALB2 / regulation of DNA damage checkpoint / XY body / mitotic G2/M transition checkpoint / postreplication repair / centrosome cycle / RNA polymerase binding / DNA repair complex / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / intracellular membraneless organelle / DNA-binding transcription activator activity / Impaired BRCA2 binding to RAD51 / response to ionizing radiation / negative regulation of gene expression via chromosomal CpG island methylation / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / ubiquitin ligase complex / regulation of DNA repair / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / protein autoubiquitination / Meiotic synapsis / tubulin binding / positive regulation of DNA repair / male germ cell nucleus / cellular response to ionizing radiation / chromosome segregation / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / negative regulation of cell growth / RING-type E3 ubiquitin transferase / HDR through Homologous Recombination (HRR) / Meiotic recombination / Metalloprotease DUBs / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / ubiquitin-protein transferase activity / fatty acid biosynthetic process / KEAP1-NFE2L2 pathway / p53 binding / double-strand break repair / cellular response to tumor necrosis factor / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / Neddylation / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / nuclear body / regulation of cell cycle / transcription cis-regulatory region binding / protein ubiquitination / chromatin remodeling / ribonucleoprotein complex / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / 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 / DNA binding
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
NICKEL (II) ION / Breast cancer type 1 susceptibility protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsWilliams, R.S. / Green, R. / Glover, J.N.M.
CitationJournal: Nat Struct Biol / Year: 2001
Title: Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1.
Authors: R S Williams / R Green / J N Glover /
Abstract: The C-terminal BRCT region of BRCA1 is essential for its DNA repair, transcriptional regulation and tumor suppressor functions. Here we determine the crystal structure of the BRCT domain of human ...The C-terminal BRCT region of BRCA1 is essential for its DNA repair, transcriptional regulation and tumor suppressor functions. Here we determine the crystal structure of the BRCT domain of human BRCA1 at 2.5 A resolution. The domain contains two BRCT repeats that adopt similar structures and are packed together in a head-to-tail arrangement. Cancer-causing missense mutations occur at the interface between the two repeats and destabilize the structure. The manner by which the two BRCT repeats interact in BRCA1 may represent a general mode of interaction between homologous domains within proteins that interact to regulate the cellular response to DNA damage. The structure provides a basis to predict the structural consequences of uncharacterized BRCA1 mutations.
History
DepositionJul 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 5, 2017Group: Refinement description
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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
X: BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5902
Polymers24,5311
Non-polymers591
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.844, 114.844, 122.111
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN / BRCA1 / breast cancer 1 / early onset / breast/ovarian cancer susceptibility protein BRCA1 /


Mass: 24531.234 Da / Num. of mol.: 1 / Fragment: residues 1646-1859
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P38398
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 4.74 Å3/Da / Density % sol: 74.03 %
Crystal growTemperature: 298 K / pH: 8.5
Details: Lithium sulphate, Nickel sulphate, calcium chloride, Tris, pH 8.5,VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Temperature: 20-23 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
118 mg/mlprotein1drop
20.8 M1reservoirLi2SO4
3100 mMTris-HCl1reservoirpH8.5
42.5 mM1reservoirNiCl2
55 mM1reservoirCaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 4, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 16968 / % possible obs: 99.8 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.57 Å / % possible all: 100
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 209566 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 9.1

-
Processing

Software
NameClassification
SOLVEphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: TLS PARAMETERS FOR REFMAC: GROUP- CHAIN X,N,&W, ALL ATOMS: T TENSOR: T11: 0.3885 T22: 0.2528 T33: 0.0541 T12: 0.2422 T13: -0.0261 T23: 0.0567 L TENSOR: L11: 15.0684 L22: 14.6911 L33: 2.1404 ...Details: TLS PARAMETERS FOR REFMAC: GROUP- CHAIN X,N,&W, ALL ATOMS: T TENSOR: T11: 0.3885 T22: 0.2528 T33: 0.0541 T12: 0.2422 T13: -0.0261 T23: 0.0567 L TENSOR: L11: 15.0684 L22: 14.6911 L33: 2.1404 L12: -13.6906 L13: 4.0117 L23: -2.8964 S TENSOR: S11: 1.1964 S12: 1.4251 S13: 0.4307 S21: -1.4475 S22: -1.3203 S23: -0.2414 S31: 0.2422 S32: 0.5625 S33: 0.1239
RfactorNum. reflection% reflectionSelection details
Rfree0.302 826 5.1 %RANDOM
Rwork0.259 ---
obs0.262 16096 --
all-16096 --
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 1 115 1660
Refinement TLS params.Method: refined / Origin x: 24.4147 Å / Origin y: 58.8128 Å / Origin z: 37.1148 Å
111213212223313233
T0.3885 Å20.2422 Å2-0.0261 Å2-0.2528 Å20.0567 Å2--0.0541 Å2
L15.0684 °2-13.6906 °24.0117 °2-14.6911 °2-2.8964 °2--2.1404 °2
S1.1964 Å °1.4251 Å °0.4307 Å °-1.4475 Å °-1.3203 Å °-0.2414 Å °0.2422 Å °0.5625 Å °0.1239 Å °
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.81

+
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