› 4zux

X-ray diffraction
3.82Å resolution

SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome

Released:
DOI: 10.2210/pdb4zux/pdb
PDB entry 4zux coloured by chain, front view.
PDB entry 4zux coloured by chain, side view.
PDB entry 4zux coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for histone H2B deubiquitination by the SAGA DUB module.
Morgan MT, Haj-Yahya M, Ringel AE, Bandi P, Brik A, Wolberger C
Science 351 725-8 (2016)
PMID: 26912860

Function and Biology Details

Reaction catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
PDBe Complex ID:
PDB-CPX-118384 (preferred)
Entry contents:
9 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (11 distinct):
Histone H3.2 Chains: A, E, K, O
Molecule details ›
Chains: A, E, K, O
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F, L, P
Molecule details ›
Chains: B, F, L, P
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A type 1 Chains: C, G, M, Q
Molecule details ›
Chains: C, G, M, Q
Length: 130 amino acids
Theoretical weight: 14.11 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H, N, R
Molecule details ›
Chains: D, H, N, R
Length: 123 amino acids
Theoretical weight: 13.66 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Ubiquitin carboxyl-terminal hydrolase 8 Chains: U, Z, e, j
Molecule details ›
Chains: U, Z, e, j
Length: 472 amino acids
Theoretical weight: 53.73 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P50102 (Residues: 1-471; Coverage: 100%)
Gene names: UBP8, YM9959.05, YMR223W
Sequence domains:
Structure domains:
Transcription and mRNA export factor SUS1 Chains: V, a, f, k
Molecule details ›
Chains: V, a, f, k
Length: 96 amino acids
Theoretical weight: 11.09 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6WNK7 (Residues: 1-96; Coverage: 100%)
Gene names: SUS1, YBR111W-A
Sequence domains: Transcription factor e(y)2
Structure domains: Serum Albumin; Chain A, Domain 1
SAGA-associated factor 11 Chains: W, b, g, l
Molecule details ›
Chains: W, b, g, l
Length: 99 amino acids
Theoretical weight: 11.3 KDa
Source organism: Saccharomyces cerevisiae YJM789
Expression system: Escherichia coli
UniProt:
  • Canonical: Q03067 (Residues: 1-99; Coverage: 100%)
Gene names: SGF11, YPL047W
Sequence domains:
Ubiquitin Chains: X, c, h, m
Molecule details ›
Chains: X, c, h, m
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
SAGA-associated factor 73 Chains: Y, d, i, n
Molecule details ›
Chains: Y, d, i, n
Length: 104 amino acids
Theoretical weight: 11.54 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P53165 (Residues: 1-104; Coverage: 16%)
Gene names: SGF73, YGL066W
Sequence domains: Zinc finger domain
DNA (145-MER) Chains: I, S
Molecule details ›
Chains: I, S
Length: 145 nucleotides
Theoretical weight: 44.52 KDa
DNA (145-MER) Chains: J, T
Molecule details ›
Chains: J, T
Length: 145 nucleotides
Theoretical weight: 44.99 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 32 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P212121
Unit cell:
a: 178.804Å b: 179.174Å c: 353.819Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.234 0.256
Expression system: Escherichia coli

Quick links

Citations

32 review citations

Breaking the chains: deubiquitylating enzyme specificity begets function.
Clague et al. (2019)
31 more

13 mentions without citation

Molecular Mechanisms of DUBs Regulation in Signaling and Disease.
Li et al. (2021)
12 more