› 6djx

X-ray diffraction
4.8Å resolution

Crystal Structure of pParkin-pUb-UbcH7 complex

Released:
DOI: 10.2210/pdb6djx/pdb
PDB entry 6djx coloured by chain, front view.
PDB entry 6djx coloured by chain, side view.
PDB entry 6djx coloured by chain, top view.
Source organisms:
Primary publication:
Mechanism of parkin activation by phosphorylation.
Sauvé V, Sung G, Soya N, Kozlov G, Blaimschein N, Miotto LS, Trempe JF, Lukacs GL, Gehring K
Nat Struct Mol Biol 25 623-630 (2018)
PMID: 29967542

Function and Biology Details

Reactions catalysed: 
(1a) [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [RBR-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [RBR-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine
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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-100152 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase parkin Chain: A
Molecule details ›
Chain: A
Length: 432 amino acids
Theoretical weight: 48.75 KDa
Source organism: Bactrocera dorsalis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: A0A034W4L8 (Residues: 29-496; Coverage: 85%)
Gene names: LOC105225264, PRKN2
Sequence domains:
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.66 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P62992 (Residues: 1-76; Coverage: 49%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains: Ubiquitin family
Ubiquitin-conjugating enzyme E2 L3 Chain: C
Molecule details ›
Chain: C
Length: 159 amino acids
Theoretical weight: 18.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P68036 (Residues: 1-154; Coverage: 100%)
Gene names: UBCE7, UBCH7, UBE2L3
Sequence domains: Ubiquitin-conjugating enzyme

Ligands and Environments

1 bound ligand:
Ligand ZN 6 x ZN
1 modified residue:
Ligand SEP 2 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P3121
Unit cell:
a: 135.669Å b: 135.669Å c: 87.993Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.258 0.257 0.29
Expression systems:
  • Escherichia coli BL21
  • Escherichia coli BL21(DE3)

Quick links

Citations

24 review citations

Molecular mechanisms and physiological functions of mitophagy.
Onishi et al. (2021)
23 more

1 mention without citation

The landscape of Parkin variants reveals pathogenic mechanisms and therapeutic targets in Parkinson's disease.
Yi et al. (2019)