+Open data
-Basic information
Entry | Database: PDB / ID: 8t3y | ||||||
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Title | Structure of Bre1-nucleosome complex - state1 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/Transferase/DNA / H2B ubiquitin E3 ligase / dimer / nucleosome acidic patch binding protein / DNA BINDING PROTEIN-Transferase-DNA complex | ||||||
Function / homology | Function and homology information HULC complex / meiotic DNA double-strand break formation / telomere maintenance via recombination / mitotic intra-S DNA damage checkpoint signaling / regulation of DNA-templated DNA replication initiation / DNA replication origin binding / subtelomeric heterochromatin formation / mitotic G1 DNA damage checkpoint signaling / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase ...HULC complex / meiotic DNA double-strand break formation / telomere maintenance via recombination / mitotic intra-S DNA damage checkpoint signaling / regulation of DNA-templated DNA replication initiation / DNA replication origin binding / subtelomeric heterochromatin formation / mitotic G1 DNA damage checkpoint signaling / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / structural constituent of chromatin / ubiquitin protein ligase activity / nucleosome / nucleosome assembly / transcription by RNA polymerase II / chromosome, telomeric region / protein ubiquitination / protein heterodimerization activity / chromatin / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) synthetic construct (others) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å | ||||||
Authors | Zhao, F. / Hicks, C.W. / Wolberger, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Mechanism of histone H2B monoubiquitination by Bre1. Authors: Fan Zhao / Chad W Hicks / Cynthia Wolberger / Abstract: Monoubiquitination of histone H2B-K120/123 plays several roles in regulating transcription, DNA replication and the DNA damage response. The structure of a nucleosome in complex with the dimeric RING ...Monoubiquitination of histone H2B-K120/123 plays several roles in regulating transcription, DNA replication and the DNA damage response. The structure of a nucleosome in complex with the dimeric RING E3 ligase Bre1 reveals that one RING domain binds to the nucleosome acidic patch, where it can position the E2 ubiquitin conjugating enzyme Rad6, while the other RING domain contacts the DNA. Comparisons with H2A-specific E3 ligases suggest a general mechanism of tuning histone specificity via the non-E2-binding RING domain. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t3y.cif.gz | 307.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t3y.ent.gz | 231.3 KB | Display | PDB format |
PDBx/mmJSON format | 8t3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t3y_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8t3y_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8t3y_validation.xml.gz | 46.7 KB | Display | |
Data in CIF | 8t3y_validation.cif.gz | 71.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/8t3y ftp://data.pdbj.org/pub/pdb/validation_reports/t3/8t3y | HTTPS FTP |
-Related structure data
Related structure data | 41016MC 8t3tC 8t3wC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 10 molecules AEBFCGDHKL
#1: Protein | Mass: 15303.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897 #4: Protein | Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 #7: Protein | Mass: 12633.649 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: BRE1, YDL074C / Production host: Escherichia coli (E. coli) References: UniProt: Q07457, RING-type E3 ubiquitin transferase |
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-601 DNA Strand ... , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 44825.559 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) |
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#6: DNA chain | Mass: 45305.852 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) |
-Non-polymers , 1 types, 4 molecules
#8: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | Y |
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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
Component | Name: Bre1-nucleosome complex / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: 20 mM HEPES, pH 7.5, 50 mM NaCl, 1 mM DTT | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Crosslinked with glutaraldehyde | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1250 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Image recording | Electron dose: 50.02 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83608 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||
Refine LS restraints |
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