› 4fk5

X-ray diffraction
2.03Å resolution

Structure of the SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module

Released:
DOI: 10.2210/pdb4fk5/pdb
PDB entry 4fk5 coloured by chain, front view.
PDB entry 4fk5 coloured by chain, side view.
PDB entry 4fk5 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 tetramer (preferred)
PDBe Complex ID:
PDB-CPX-546473 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Ubiquitin carboxyl-terminal hydrolase 8 Chain: A
Molecule details ›
Chain: A
Length: 476 amino acids
Theoretical weight: 54.06 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 Chain: B
Molecule details ›
Chain: B
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 Chain: C
Molecule details ›
Chain: C
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:
SAGA-associated factor 73 Chain: E
Molecule details ›
Chain: E
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

3 bound ligands:
Ligand ZN 8 x ZN
Ligand GOL 2 x GOL
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 83.528Å b: 104.775Å c: 107.018Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.175 0.212
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

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

1 mention without citation

A role for intersubunit interactions in maintaining SAGA deubiquitinating module structure and activity.
Samara et al. (2012)