› 2eke

X-ray diffraction
1.9Å resolution

Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a noncovalent Ubiquitin-like protein-E2 complex as a platform for selective interactions within a SUMO pathway

Released:
DOI: 10.2210/pdb2eke/pdb
PDB entry 2eke coloured by chain, front view.
PDB entry 2eke coloured by chain, side view.
PDB entry 2eke coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a non-covalent ubiquitin-like protein-E2 complex as a platform for selective interactions within a SUMO pathway.
Duda DM, van Waardenburg RC, Borg LA, McGarity S, Nourse A, Waddell MB, Bjornsti MA, Schulman BA
J Mol Biol 369 619-30 (2007)
PMID: 17475278

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156250 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
SUMO-conjugating enzyme UBC9 Chains: A, B
Molecule details ›
Chains: A, B
Length: 157 amino acids
Theoretical weight: 17.94 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P50623 (Residues: 1-157; Coverage: 100%)
Gene names: UBC9, YDL064W
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin-like protein SMT3 Chains: C, D
Molecule details ›
Chains: C, D
Length: 106 amino acids
Theoretical weight: 12.19 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12306 (Residues: 13-98; Coverage: 85%)
Gene names: D9719.15, SMT3, YDR510W
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: C2
Unit cell:
a: 120.891Å b: 84.578Å c: 80.141Å
α: 90° β: 124.31° γ: 90°
R-values:
R R work R free
0.244 0.225 0.25
Expression system: Escherichia coli

Quick links

Citations

7 review citations

The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition.
Gareau et al. (2010)
6 more

10 mentions without citation

E2s: structurally economical and functionally replete.
Wenzel et al. (2011)
9 more