› 6djw

X-ray diffraction
3.8Å resolution

Crystal Structure of pParkin (REP and RING2 deleted)-pUb-UbcH7 complex

Released:
DOI: 10.2210/pdb6djw/pdb
PDB entry 6djw coloured by chain, front view.
PDB entry 6djw coloured by chain, side view.
PDB entry 6djw 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: 349 amino acids
Theoretical weight: 39.41 KDa
Source organism: Bactrocera dorsalis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A034W4L8 (Residues: 29-412; Coverage: 69%)
Gene names: LOC105225264, PRKN2
Sequence domains:
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 74 amino acids
Theoretical weight: 8.54 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P62992 (Residues: 1-74; Coverage: 47%)
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
Structure 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: 134.606Å b: 134.606Å c: 86.193Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.265 0.263 0.297
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

23 review citations

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

4 mentions without citation

Chain reactions: molecular mechanisms of RBR ubiquitin ligases.
Cotton et al. (2020)
3 more