PDBe 4dhj

X-ray diffraction
2.35Å resolution

The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex

Released:
Primary publication:
The mechanism of OTUB1-mediated inhibition of ubiquitination.
OpenAccess logo 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:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
monomeric
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Ubiquitin thioesterase otubain-like Chains: A, E, I, L
Molecule details ›
Chains: A, E, I, L
Length: 284 amino acids
Theoretical weight: 32.32 KDa
Source organism: Caenorhabditis elegans
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9XVR6 (Residues: 1-284; Coverage: 100%)
Gene names: C25D7.8, otub-1
Sequence domains: Peptidase C65 Otubain
Structure domains:
Ubiquitin Chains: B, F, J, M
Molecule details ›
Chains: B, F, J, M
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 Chains: D, H
Molecule details ›
Chains: D, H
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 Chains: C, G, K, N
Molecule details ›
Chains: C, G, K, N
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:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 68.45Å b: 182.815Å c: 242.768Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.203 0.237
Expression system: Escherichia coli