› 6pgv

X-ray diffraction
2.3Å resolution

Human Josephin-2 in complex with ubiquitin

Released:
DOI: 10.2210/pdb6pgv/pdb
PDB entry 6pgv coloured by chain, front view.
PDB entry 6pgv coloured by chain, side view.
PDB entry 6pgv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into the activity and regulation of human Josephin-2
Grasty KC, Weeks SD, Loll PJ
J. Struct. Biol. 3 100011- (2019)

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143284 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Josephin-2 Chain: A
Molecule details ›
Chain: A
Length: 188 amino acids
Theoretical weight: 20.87 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8TAC2 (Residues: 1-188; Coverage: 100%)
Gene names: JOSD2, SBBI54
Sequence domains: Josephin
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 75 amino acids
Theoretical weight: 8.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG47 (Residues: 153-227; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand NEH 1 x NEH
1 modified residue:
Ligand MSE 2 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Spacegroup: P6122
Unit cell:
a: 102.12Å b: 102.12Å c: 92.2Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.201 0.201 0.224
Expression system: Escherichia coli BL21(DE3)

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