› 4dhz

X-ray diffraction
3.11Å resolution

The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub

Released:
DOI: 10.2210/pdb4dhz/pdb
PDB entry 4dhz coloured by chain, front view.
PDB entry 4dhz coloured by chain, side view.
PDB entry 4dhz coloured by chain, top view.
Source organisms:
Primary publication:
The mechanism of OTUB1-mediated inhibition of ubiquitination.
Wiener R, Zhang X, Wang T, Wolberger C
Nature 483 618-22 (2012)
PMID: 22367539

Function and Biology Details

Reactions 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).
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
monomeric
PDBe Complex ID:
PDB-CPX-219251 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Ubiquitin thioesterase OTUB1; Ubiquitin thioesterase otubain-like Chain: A
Molecule details ›
Chain: A
Length: 288 amino acids
Theoretical weight: 32.8 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: Q96FW1 (Residues: 1-48; Coverage: 18%)
  • Canonical: Q9XVR6 (Residues: 45-284; Coverage: 85%)
Gene names: C25D7.8, HSPC263, OTB1, OTU1, OTUB1, otub-1
Sequence domains: Peptidase C65 Otubain
Structure domains:
Ubiquitin Chain: B
Molecule details ›
Chain: B
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
Ubiquitin Chain: E
Molecule details ›
Chain: E
Length: 76 amino acids
Theoretical weight: 8.62 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
Ubiquitin-conjugating enzyme E2 N Chain: F
Molecule details ›
Chain: F
Length: 152 amino acids
Theoretical weight: 17.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61088 (Residues: 1-152; Coverage: 100%)
Gene names: BLU, UBE2N
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme

Ligands and Environments

No bound ligands
1 modified residue:
Ligand GLZ 1 x GLZ

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P41
Unit cell:
a: 123.371Å b: 123.371Å c: 68.653Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.236 0.233 0.288
Expression system: Escherichia coli

Quick links

Citations

48 review citations

Regulation of DNA damage responses by ubiquitin and SUMO.
Jackson et al. (2013)
47 more

8 mentions without citation

Ubc13: the Lys63 ubiquitin chain building machine.
Hodge et al. (2016)
7 more