› 3mhs

X-ray diffraction
1.89Å resolution

Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde

Released:
DOI: 10.2210/pdb3mhs/pdb
PDB entry 3mhs coloured by chain, front view.
PDB entry 3mhs coloured by chain, side view.
PDB entry 3mhs coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into the assembly and function of the SAGA deubiquitinating module.
Samara NL, Datta AB, Berndsen CE, Zhang X, Yao T, Cohen RE, Wolberger C
Science 328 1025-9 (2010)
PMID: 20395473

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 pentamer (preferred)
PDBe Complex ID:
PDB-CPX-143355 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Ubiquitin carboxyl-terminal hydrolase 8 Chain: A
Molecule details ›
Chain: A
Length: 476 amino acids
Theoretical weight: 54.03 KDa
Source organism: Saccharomyces cerevisiae
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 Chain: B
Molecule details ›
Chain: B
Length: 96 amino acids
Theoretical weight: 11.09 KDa
Source organism: Saccharomyces cerevisiae
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 Chain: C
Molecule details ›
Chain: C
Length: 99 amino acids
Theoretical weight: 11.3 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q03067 (Residues: 1-99; Coverage: 100%)
Gene names: SGF11, YPL047W
Sequence domains:
Structure domains:
Ubiquitin Chain: D
Molecule details ›
Chain: D
Length: 76 amino acids
Theoretical weight: 8.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
SAGA-associated factor 73 Chain: E
Molecule details ›
Chain: E
Length: 96 amino acids
Theoretical weight: 10.82 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P53165 (Residues: 1-96; Coverage: 15%)
Gene names: SGF73, YGL066W
Sequence domains: Zinc finger domain

Ligands and Environments

3 bound ligands:
Ligand EDO 1 x EDO
Ligand GOL 1 x GOL
Ligand ZN 8 x ZN
1 modified residue:
Ligand GLZ 1 x GLZ

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 78.6Å b: 102.084Å c: 120.903Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.159 0.208
Expression system: Escherichia coli

Quick links

Citations

32 review citations

Deubiquitylases from genes to organism.
Clague et al. (2013)
31 more

18 mentions without citation

Synthetic and semi-synthetic strategies to study ubiquitin signaling.
van Tilburg et al. (2016)
17 more