› 4fjc

X-ray diffraction
2.83Å resolution

Structure of the SAGA Ubp8/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module

Released:
DOI: 10.2210/pdb4fjc/pdb
PDB entry 4fjc coloured by chain, front view.
PDB entry 4fjc coloured by chain, side view.
PDB entry 4fjc coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
A role for intersubunit interactions in maintaining SAGA deubiquitinating module structure and activity.
Samara NL, Ringel AE, Wolberger C
Structure 20 1414-24 (2012)
PMID: 22771212

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 octamer (preferred)
PDBe Complex ID:
PDB-CPX-156127 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Ubiquitin carboxyl-terminal hydrolase 8 Chains: A, E
Molecule details ›
Chains: A, E
Length: 476 amino acids
Theoretical weight: 54.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
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: B, F
Molecule details ›
Chains: B, F
Length: 96 amino acids
Theoretical weight: 11.09 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
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: C, G
Molecule details ›
Chains: C, G
Length: 99 amino acids
Theoretical weight: 11.3 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q03067 (Residues: 1-99; Coverage: 100%)
Gene names: SGF11, YPL047W
Sequence domains:
Structure domains: Helix Hairpins
SAGA-associated factor 73 Chains: D, H
Molecule details ›
Chains: D, H
Length: 96 amino acids
Theoretical weight: 10.82 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P53165 (Residues: 1-96; Coverage: 15%)
Gene names: SGF73, YGL066W
Sequence domains: Zinc finger domain

Ligands and Environments

2 bound ligands:
Ligand ZN 14 x ZN
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 76.49Å b: 79.202Å c: 265.943Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.2 0.276
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Sharing the SAGA.
Helmlinger et al. (2017)
3 more

2 mentions without citation

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