ISDA: 8T3T

Deposition Date 2023-06-07

Release Date 2023-10-18

Last Version Date 2023-11-22

Entry Detail

PDB ID:

8T3T

Keywords:

DNA BINDING PROTEIN/Transferase/DNA

Title:

Structure of Bre1-nucleosome complex - state3

Biological Source:

Source Organism(s):

Xenopus laevis (Taxon ID: 8355)
Saccharomyces cerevisiae (Taxon ID: 4932)
synthetic construct (Taxon ID: 32630)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.21 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

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

Structures with similar UniProt ID

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

Structures with similar UniProt ID

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

Structures with similar UniProt ID

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

Structures with similar UniProt ID

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

Primary Citation

Mechanism of histone H2B monoubiquitination by Bre1.

Zhao, F, Hicks, C.W, Wolberger, C.Show

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

Abstact

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