8T3W image
Deposition Date 2023-06-07
Release Date 2023-10-18
Last Version Date 2023-11-22
Entry Detail
PDB ID:
8T3W
Keywords:
DNA BINDING PROTEIN/Transferase/DNA
Title:
Structure of Bre1-nucleosome complex - state2
Biological Source:
Source Organism:
Xenopus laevis (Taxon ID: 8355)
synthetic construct (Taxon ID: 32630)
Saccharomyces cerevisiae (Taxon ID: 4932)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.25 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8T3W validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Chain IDs:A, E
Chain Length:135
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P84233 Pfam ID:PF00125
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:B, F
Chain Length:102
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P62799 Pfam ID:PF15511
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1
Chain IDs:C, G
Chain Length:129
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P06897 Pfam ID:PF00125, PF16211
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B
Chain IDs:D, H
Chain Length:122
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P02281 Pfam ID:PF00125
Polymer Type:polydeoxyribonucleotide
Molecule:601 DNA strand 1
Chain IDs:I
Chain Length:146
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:601 DNA strand 2
Chain IDs:J
Chain Length:146
Number of Molecules:1
Biological Source:synthetic construct
Protein Blast
Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase BRE1
Gene (Uniprot):BRE1
Chain IDs:K, L
Chain Length:110
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q07457 Pfam ID:PF00097
Ligand Molecules
ZN
Primary Citation
Mechanism of histone H2B monoubiquitination by Bre1.
Nat.Struct.Mol.Biol. 30 1623 1627 (2023)
PMID: 37872231 DOI: 10.1038/s41594-023-01137-x

Abstact

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.

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Primary Citation of related structures
8T3W