› 6crn

X-ray diffraction
2.5Å resolution

Structure of the USP15 deubiquitinase domain in complex with a high-affinity first-generation Ubv

Released:
DOI: 10.2210/pdb6crn/pdb
PDB entry 6crn coloured by chain, front view.
PDB entry 6crn coloured by chain, side view.
PDB entry 6crn coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15.
Teyra J, Singer AU, Schmitges FW, Jaynes P, Kit Leng Lui S, Polyak MJ, Fodil N, Krieger JR, Tong J, Schwerdtfeger C, Brasher BB, Ceccarelli DFJ, Moffat J, Sicheri F, Moran MF, Gros P, Eichhorn PJA, Lenter M, Boehmelt G, Sidhu SS
Structure 27 590-605.e5 (2019)
PMID: 30713027

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-166554 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin carboxyl-terminal hydrolase 15 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 360 amino acids
Theoretical weight: 40.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y4E8 (Residues: 275-934; Coverage: 36%)
Gene names: KIAA0529, USP15
Sequence domains: Ubiquitin carboxyl-terminal hydrolase
Structure domains: Cysteine proteinases
Ubiquitin variant 15.2 Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 81 amino acids
Theoretical weight: 9.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P1
Unit cell:
a: 41.77Å b: 98.942Å c: 122.043Å
α: 66.49° β: 88.31° γ: 78.1°
R-values:
R R work R free
0.19 0.188 0.236
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Regulation of Wnt Signaling through Ubiquitination and Deubiquitination in Cancers.
Park et al. (2020)
9 more

2 mentions without citation

Ubiquitin Engineering for Interrogating the Ubiquitin-Proteasome System and Novel Therapeutic Strategies.
Tang et al. (2023)
1 more