› 6isu

X-ray diffraction
1.87Å resolution

Crystal structure of Lys27-linked di-ubiquitin in complex with its selective interacting protein UCHL3

Released:
DOI: 10.2210/pdb6isu/pdb
PDB entry 6isu coloured by chain, front view.
PDB entry 6isu coloured by chain, side view.
PDB entry 6isu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Chemical Protein Synthesis Enabled Mechanistic Studies on the Molecular Recognition of K27-linked Ubiquitin Chains.
Pan M, Zheng Q, Ding S, Zhang L, Qu Q, Wang T, Hong D, Ren Y, Liang L, Chen C, Mei Z, Liu L
Angew Chem Int Ed Engl 58 2627-2631 (2019)
PMID: 30589182

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143235 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin carboxyl-terminal hydrolase isozyme L3 Chain: A
Molecule details ›
Chain: A
Length: 230 amino acids
Theoretical weight: 26.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P15374 (Residues: 1-230; Coverage: 100%)
Gene name: UCHL3
Sequence domains: Ubiquitin carboxyl-terminal hydrolase, family 1
Structure domains: Peptidase C12, ubiquitin carboxyl-terminal hydrolase
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
Ubiquitin Chain: C
Molecule details ›
Chain: C
Length: 76 amino acids
Theoretical weight: 8.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17B1
Spacegroup: C2221
Unit cell:
a: 91.407Å b: 94.204Å c: 91.178Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.209 0.264
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Chemoenzymatic Semisynthesis of Proteins.
Thompson et al. (2020)
4 more