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- PDB-8grq: Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome -

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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 / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function ...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 / 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 / BRCA1-B complex / BRCA1-A complex / UCH proteinases / negative regulation of centriole replication / sex-chromosome dosage compensation / random inactivation of X chromosome / negative regulation of intracellular estrogen receptor signaling pathway / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / chordate embryonic development / negative regulation of fatty acid biosynthetic process / cellular response to indole-3-methanol / DNA strand resection involved in replication fork processing / homologous recombination / lateral element / tissue homeostasis / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / Ub-specific processing proteases / Impaired BRCA2 binding to PALB2 / XY body / regulation of phosphorylation / mitotic G2/M transition checkpoint / negative regulation of protein export from nucleus / DNA repair complex / centrosome cycle / postreplication repair / RNA polymerase binding / 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) / DNA-binding transcription activator activity / Impaired BRCA2 binding to RAD51 / intracellular membraneless organelle / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / 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 / protein autoubiquitination / regulation of DNA repair / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ubiquitin ligase complex / nucleosomal DNA binding / Meiotic synapsis / positive regulation of DNA repair / tubulin binding / male germ cell nucleus / chromosome segregation / TP53 Regulates Transcription of DNA Repair Genes / cellular response to ionizing radiation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / negative regulation of cell growth / HDR through Homologous Recombination (HRR) / heterochromatin formation / Metalloprotease DUBs / Meiotic recombination / kinase binding / fatty acid biosynthetic process / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / structural constituent of chromatin / intrinsic apoptotic signaling pathway in response to DNA damage / UCH proteinases / KEAP1-NFE2L2 pathway / nucleosome / p53 binding / double-strand break repair / nucleosome assembly / cellular response to tumor necrosis factor
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 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain ...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 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / BRCT domain profile. / BRCT domain / BRCT domain superfamily / 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 / Histone H3 signature 1. / Ankyrin repeat / Zinc finger RING-type profile. / Histone H3 signature 2. / Histone H3 / Zinc finger, RING-type / Histone H3/CENP-A / Ankyrin repeat-containing domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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)

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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)

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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

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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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

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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)

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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

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