[English] 日本語
Yorodumi
- PDB-8grq: Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8grq
TitleCryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome
Components
  • (DNA (147-MER)) x 2
  • BRCA1-associated RING domain protein 1
  • Breast cancer type 1 susceptibility protein
  • H2B
  • Histone H2A type 1-H
  • Histone H3
  • Histone H4
  • Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a
KeywordsNUCLEAR PROTEIN / nucleosome / BRCA1/BARD1 / BRCA1 / BARD1 / H2AK127 / H2AK127-UbcH5c-Ub
Function / homology
Function and homology information


negative regulation of mRNA 3'-end processing / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / DNA Damage/Telomere Stress Induced Senescence / Regulation of endogenous retroelements by KRAB-ZFP proteins / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / Cleavage of the damaged purine / histone H2AK127 ubiquitin ligase activity / histone H2AK129 ubiquitin ligase activity ...negative regulation of mRNA 3'-end processing / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / DNA Damage/Telomere Stress Induced Senescence / Regulation of endogenous retroelements by KRAB-ZFP proteins / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / Cleavage of the damaged purine / 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 / Metalloprotease DUBs / BRCA1-BARD1 complex / HDACs deacetylate histones / PRC2 methylates histones and DNA / BRCA1-C complex / UCH proteinases / BRCA1-B complex / BRCA1-A complex / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / negative regulation of centriole replication / sex-chromosome dosage compensation / negative regulation of intracellular estrogen receptor signaling pathway / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / random inactivation of X chromosome / RMTs methylate histone arginines / 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 / tissue homeostasis / protein K6-linked ubiquitination / Ub-specific processing proteases / regulation of phosphorylation / Impaired BRCA2 binding to PALB2 / regulation of DNA damage checkpoint / XY body / mitotic G2/M transition checkpoint / negative regulation of protein export from nucleus / 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 / kinase binding / Metalloprotease DUBs / cytoplasmic ribonucleoprotein granule / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of angiogenesis / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / fatty acid biosynthetic process / structural constituent of chromatin / UCH proteinases / KEAP1-NFE2L2 pathway / p53 binding / nucleosome / double-strand break repair
Similarity search - Function
BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Histone, subunit A / Histone, subunit A ...BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Histone, subunit A / Histone, subunit A / 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 / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Histone H3 signature 1. / Ankyrin repeat-containing domain superfamily / Zinc finger RING-type profile. / Histone H3 signature 2. / Zinc finger, RING-type / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H4 / Histone H3 / Breast cancer type 1 susceptibility protein / Histone H2A type 1-H / BRCA1-associated RING domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsAi, H.S. / Zebin, T. / Zhiheng, D. / Jiakun, T. / Liying, Z. / Jia-Bin, L. / Man, P. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 81621002 and 21977090 China
CitationJournal: Chem / Year: 2023
Title: Synthetic E2-Ub-nucleosome conjugates for studying nucleosome ubiquitination.
Authors: Ai, H.S. / Tong, Z. / Deng, Z. / Tian, J. / Zhang, L. / Sun, M. / Du, Y. / Xu, Z. / Shi, Q. / Liang, L. / Zheng, Q. / Li, J.B. / Pan, M. / Liu, L.
History
DepositionSep 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A type 1-H
D: H2B
E: Histone H3
F: Histone H4
G: Histone H2A type 1-H
H: H2B
I: DNA (147-MER)
J: DNA (147-MER)
K: Breast cancer type 1 susceptibility protein
M: BRCA1-associated RING domain protein 1
N: Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,96117
Polymers235,69913
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 7 types, 11 molecules AEBFCGDHKMN

#1: Protein Histone H3


Mass: 11530.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALMAC_LOCUS17614 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A653DHJ5
#2: Protein Histone H4


Mass: 9123.692 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Dana\GF27365, Dana_GF27365, GF27365 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P9AXL3
#3: Protein Histone H2A type 1-H / H2A-clustered histone 12


Mass: 12066.128 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2ac12, Hist1h2ah / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CGP6
#4: Protein H2B


Mass: 20937.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#7: Protein Breast cancer type 1 susceptibility protein / RING finger protein 53 / RING-type E3 ubiquitin transferase BRCA1


Mass: 10626.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / Production host: Escherichia coli (E. coli)
References: UniProt: P38398, RING-type E3 ubiquitin transferase
#8: Protein BRCA1-associated RING domain protein 1 / BARD-1 / RING-type E3 ubiquitin transferase BARD1


Mass: 10348.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BARD1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99728, RING-type E3 ubiquitin transferase
#9: Protein Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a


Mass: 16657.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D3, hCG_2028213 / Production host: Escherichia coli (E. coli)

-
DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (147-MER)


Mass: 45604.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (147-MER)


Mass: 45145.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 1 types, 4 molecules

#10: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Complex of BRCA1/BARD1 and H2AK127-UbcH5c-Ub nucleosome
Type: COMPLEX / Entity ID: #9, #1-#3, #5-#6, #4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68006 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415439
ELECTRON MICROSCOPYf_angle_d0.74222124
ELECTRON MICROSCOPYf_dihedral_angle_d31.9994149
ELECTRON MICROSCOPYf_chiral_restr0.0422524
ELECTRON MICROSCOPYf_plane_restr0.0061792

+
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