› 2knb

Solution NMR

Solution NMR structure of the parkin Ubl domain in complex with the endophilin-A1 SH3 domain

Released:
DOI: 10.2210/pdb2knb/pdb
PDB entry 2knb coloured by chain, ensemble of 20 models, front view.
PDB entry 2knb coloured by chain, ensemble of 20 models, side view.
PDB entry 2knb coloured by chain, ensemble of 20 models, top view.
Source organism: Rattus norvegicus
Primary publication:
SH3 domains from a subset of BAR proteins define a Ubl-binding domain and implicate parkin in synaptic ubiquitination.
Trempe JF, Chen CX, Grenier K, Camacho EM, Kozlov G, McPherson PS, Gehring K, Fon EA
Mol Cell 36 1034-47 (2009)
PMID: 20064468

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128653 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase parkin Chain: A
Molecule details ›
Chain: A
Length: 81 amino acids
Theoretical weight: 9.15 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9JK66 (Residues: 1-76; Coverage: 16%)
Gene names: Park2, Prkn
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Endophilin-A1 Chain: B
Molecule details ›
Chain: B
Length: 71 amino acids
Theoretical weight: 7.98 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: O35179 (Residues: 291-352; Coverage: 18%)
Gene names: Sh3d2a, Sh3gl2, Sh3p4
Sequence domains: SH3 domain
Structure domains: SH3 Domains

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Refinement method: simulated annealing
Expression system: Escherichia coli

Quick links

Citations

34 review citations

What genetics tells us about the causes and mechanisms of Parkinson's disease.
Corti et al. (2011)
33 more

1 mention without citation

PINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating Serine 65.
Kondapalli et al. (2012)