4ZUX image
Deposition Date 2015-05-17
Release Date 2016-02-24
Last Version Date 2024-11-20
Entry Detail
PDB ID:
4ZUX
Keywords:
Title:
SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome
Biological Source:
Method Details:
Experimental Method:
Resolution:
3.82 Å
R-Value Free:
0.25
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Chain IDs:A, E, K, O
Chain Length:136
Number of Molecules:4
Biological Source:Xenopus laevis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:B, F, L, P
Chain Length:99
Number of Molecules:4
Biological Source:Xenopus laevis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1
Chain IDs:C, G, M, Q
Chain Length:76
Number of Molecules:4
Biological Source:Xenopus laevis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B 1.1
Chain IDs:D, H, N, R
Chain Length:123
Number of Molecules:4
Biological Source:Xenopus laevis
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (145-MER)
Chain IDs:I, S
Chain Length:145
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (145-MER)
Chain IDs:J, T
Chain Length:472
Number of Molecules:2
Biological Source:synthetic construct
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin carboxyl-terminal hydrolase 8
Gene (Uniprot):UBP8
Chain IDs:U, Z, EA (auth: e), JA (auth: j)
Chain Length:472
Number of Molecules:4
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription and mRNA export factor SUS1
Gene (Uniprot):SUS1
Chain IDs:V, AA (auth: a), FA (auth: f), KA (auth: k)
Chain Length:136
Number of Molecules:4
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SAGA-associated factor 11
Chain IDs:W, BA (auth: b), GA (auth: g), LA (auth: l)
Chain Length:99
Number of Molecules:4
Biological Source:Saccharomyces cerevisiae (strain YJM789)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Polyubiquitin-B
Gene (Uniprot):UBB
Chain IDs:X, CA (auth: c), HA (auth: h), MA (auth: m)
Chain Length:76
Number of Molecules:4
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SAGA-associated factor 73
Gene (Uniprot):SGF73
Chain IDs:Y, DA (auth: d), IA (auth: i), NA (auth: n)
Chain Length:123
Number of Molecules:4
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Ligand Molecules
Primary Citation
Structural basis for histone H2B deubiquitination by the SAGA DUB module.
Science 351 725 728 (2016)
PMID: 26912860 DOI: 10.1126/science.aac5681

Abstact

Monoubiquitinated histone H2B plays multiple roles in transcription activation. H2B is deubiquitinated by the Spt-Ada-Gcn5 acetyltransferase (SAGA) coactivator, which contains a four-protein subcomplex known as the deubiquitinating (DUB) module. The crystal structure of the Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to a ubiquitinated nucleosome reveals that the DUB module primarily contacts H2A/H2B, with an arginine cluster on the Sgf11 zinc finger domain docking on the conserved H2A/H2B acidic patch. The Ubp8 catalytic domain mediates additional contacts with H2B, as well as with the conjugated ubiquitin. We find that the DUB module deubiquitinates H2B both in the context of the nucleosome and in H2A/H2B dimers complexed with the histone chaperone, FACT, suggesting that SAGA could target H2B at multiple stages of nucleosome disassembly and reassembly during transcription.

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Primary Citation of related structures