› 2znv

X-ray diffraction
1.6Å resolution

Crystal structure of human AMSH-LP DUB domain in complex with Lys63-linked ubiquitin dimer

Released:
DOI: 10.2210/pdb2znv/pdb
PDB entry 2znv coloured by chain, front view.
PDB entry 2znv coloured by chain, side view.
PDB entry 2znv coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains.
Sato Y, Yoshikawa A, Yamagata A, Mimura H, Yamashita M, Ookata K, Nureki O, Iwai K, Komada M, Fukai S
Nature 455 358-62 (2008)
PMID: 18758443

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188497 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
AMSH-like protease Chains: A, D
Molecule details ›
Chains: A, D
Length: 178 amino acids
Theoretical weight: 19.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96FJ0 (Residues: 264-436; Coverage: 40%)
Gene names: AMSHLP, KIAA1373, STAMBPL1
Sequence domains: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
Structure domains: Cytidine Deaminase, domain 2
Ubiquitin Chains: B, E
Molecule details ›
Chains: B, E
Length: 76 amino acids
Theoretical weight: 8.6 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG50 (Residues: 609-684; Coverage: 10%)
Gene name: Ubc
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Ubiquitin Chains: C, F
Molecule details ›
Chains: C, F
Length: 77 amino acids
Theoretical weight: 8.69 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG50 (Residues: 609-684; Coverage: 10%)
Gene name: Ubc
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21
Unit cell:
a: 38.089Å b: 97.363Å c: 87.894Å
α: 90° β: 97.49° γ: 90°
R-values:
R R work R free
0.185 0.184 0.215
Expression system: Escherichia coli

Quick links

Citations

61 review citations

The ubiquitin code.
Komander et al. (2012)
60 more

32 mentions without citation

Regulation of proteolysis by human deubiquitinating enzymes.
Eletr et al. (2014)
31 more