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Yorodumi- PDB-7jzv: Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to... -
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-Basic information
Entry | Database: PDB / ID: 7jzv | ||||||
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Title | Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome | ||||||
Components |
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Keywords | LIGASE/DNA / Complex / Ubiquitin / Nucleosome / RING / ligase / LIGASE-DNA complex | ||||||
Function / homology | Function and homology information negative regulation of mRNA 3'-end processing / 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 / random inactivation of X chromosome / negative regulation of centriole replication ...negative regulation of mRNA 3'-end processing / 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 / random inactivation of X chromosome / negative regulation of centriole replication / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / chordate embryonic development / negative regulation of fatty acid biosynthetic process / (E3-independent) E2 ubiquitin-conjugating enzyme / cellular response to indole-3-methanol / homologous recombination / lateral element / tissue homeostasis / XY body / protein K6-linked ubiquitination / Signaling by BMP / regulation of DNA damage checkpoint / regulation of phosphorylation / dosage compensation by inactivation of X chromosome / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to PALB2 / protein K11-linked ubiquitination / : / mitotic G2/M transition checkpoint / negative regulation of protein export from nucleus / postreplication repair / DNA repair complex / RNA polymerase binding / centrosome cycle / 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 / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / intracellular non-membrane-bounded organelle / response to ionizing radiation / DNA-binding transcription activator activity / ubiquitin conjugating enzyme activity / Transcriptional Regulation by E2F6 / protein monoubiquitination / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of BMP signaling pathway / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / protein K48-linked ubiquitination / localization / negative regulation of megakaryocyte differentiation / regulation of DNA repair / protein autoubiquitination / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / ubiquitin ligase complex / SUMOylation of DNA damage response and repair proteins / Packaging Of Telomere Ends / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / positive regulation of DNA repair / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / tubulin binding / TICAM1, RIP1-mediated IKK complex recruitment / DNA methylation / IKK complex recruitment mediated by RIP1 / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / male germ cell nucleus / Defective pyroptosis / Negative regulators of DDX58/IFIH1 signaling / chromosome segregation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Witus, S.R. / Burrell, A.L. / Hansen, J.M. / Farrell, D.P. / Dimaio, F. / Kollman, J.M. / Klevit, R.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1. Authors: Samuel R Witus / Anika L Burrell / Daniel P Farrell / Jianming Kang / Meiling Wang / Jesse M Hansen / Alex Pravat / Lisa M Tuttle / Mikaela D Stewart / Peter S Brzovic / Champak Chatterjee / ...Authors: Samuel R Witus / Anika L Burrell / Daniel P Farrell / Jianming Kang / Meiling Wang / Jesse M Hansen / Alex Pravat / Lisa M Tuttle / Mikaela D Stewart / Peter S Brzovic / Champak Chatterjee / Weixing Zhao / Frank DiMaio / Justin M Kollman / Rachel E Klevit / Abstract: Mutations in the E3 ubiquitin ligase RING domains of BRCA1/BARD1 predispose carriers to breast and ovarian cancers. We present the structure of the BRCA1/BARD1 RING heterodimer with the E2 enzyme ...Mutations in the E3 ubiquitin ligase RING domains of BRCA1/BARD1 predispose carriers to breast and ovarian cancers. We present the structure of the BRCA1/BARD1 RING heterodimer with the E2 enzyme UbcH5c bound to its cellular target, the nucleosome, along with biochemical data that explain how the complex selectively ubiquitylates lysines 125, 127 and 129 in the flexible C-terminal tail of H2A in a fully human system. The structure reveals that a novel BARD1-histone interface couples to a repositioning of UbcH5c compared to the structurally similar PRC1 E3 ligase Ring1b/Bmi1 that ubiquitylates H2A Lys119 in nucleosomes. This interface is sensitive to both H3 Lys79 methylation status and mutations found in individuals with cancer. Furthermore, NMR reveals an unexpected mode of E3-mediated substrate regulation through modulation of dynamics in the C-terminal tail of H2A. Our findings provide insight into how E3 ligases preferentially target nearby lysine residues in nucleosomes by a steric occlusion and distancing mechanism. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7jzv.cif.gz | 335.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jzv.ent.gz | 245.5 KB | Display | PDB format |
PDBx/mmJSON format | 7jzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/7jzv ftp://data.pdbj.org/pub/pdb/validation_reports/jz/7jzv | HTTPS FTP |
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-Related structure data
Related structure data | 22581MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 6 types, 10 molecules ABNnOoPpQq
#1: Protein | Mass: 28974.465 Da / Num. of mol.: 1 / Mutation: UbcH5c C85K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, UBE2D3, UBC5C, UBCH5C / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A386IN42, UniProt: P61077, UniProt: P38398*PLUS, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme, RING-type E3 ubiquitin transferase | ||||||
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#2: Protein | Mass: 12983.018 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 BL21(DE3) (bacteria) References: UniProt: Q99728, RING-type E3 ubiquitin transferase | ||||||
#3: Protein | Mass: 14310.728 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: H2AC18, H2AFO, HIST2H2AA, HIST2H2AA3, H2AC19, HIST2H2AA4 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6FI13 #4: Protein | Mass: 13790.018 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC12, H2BFT, HIRIP1, HIST1H2BK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60814 #5: Protein | Mass: 15257.838 Da / Num. of mol.: 2 / Mutation: C110A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q71DI3 #6: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62805 |
-Widom 601 153- ... , 2 types, 2 molecules XY
#7: DNA chain | Mass: 47457.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a |
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#8: DNA chain | Mass: 46998.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a |
-Non-polymers , 1 types, 4 molecules
#9: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
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Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 90 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 |
Image scans | Movie frames/image: 50 / Used frames/image: 1-50 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21479 / Symmetry type: POINT |