› 3m63

X-ray diffraction
2.4Å resolution

Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Dsk2

Released:
DOI: 10.2210/pdb3m63/pdb
PDB entry 3m63 coloured by chain, front view.
PDB entry 3m63 coloured by chain, side view.
PDB entry 3m63 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
The yeast E4 ubiquitin ligase Ufd2 interacts with the ubiquitin-like domains of Rad23 and Dsk2 via a novel and distinct ubiquitin-like binding domain.
Hänzelmann P, Stingele J, Hofmann K, Schindelin H, Raasi S
J Biol Chem 285 20390-8 (2010)
PMID: 20427284

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155747 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E4 ubiquitin-protein ligase UFD2 Chain: A
Molecule details ›
Chain: A
Length: 968 amino acids
Theoretical weight: 110.81 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P54860 (Residues: 1-961; Coverage: 100%)
Gene names: D1255, UFD2, YDL190C
Sequence domains:
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Ubiquitin domain-containing protein DSK2 Chain: B
Molecule details ›
Chain: B
Length: 101 amino acids
Theoretical weight: 11.54 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P48510 (Residues: 1-75; Coverage: 20%)
Gene names: DSK2, SHE4, YM8021.02, YMR276W
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

2 bound ligands:
Ligand 1PE 1 x 1PE
Ligand K 1 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P212121
Unit cell:
a: 65.13Å b: 125.7Å c: 181.21Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.206 0.27
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Structure and Function of the 26S Proteasome.
Bard et al. (2018)
7 more

1 mention without citation

The yeast E4 ubiquitin ligase Ufd2 interacts with the ubiquitin-like domains of Rad23 and Dsk2 via a novel and distinct ubiquitin-like binding domain.
Hänzelmann et al. (2010)