4K95

Crystal Structure of Parkin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.499 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.307 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of parkin reveals mechanisms for ubiquitin ligase activation.

Trempe, J.F.Sauve, V.Grenier, K.Seirafi, M.Tang, M.Y.Menade, M.Al-Abdul-Wahid, S.Krett, J.Wong, K.Kozlov, G.Nagar, B.Fon, E.A.Gehring, K.

(2013) Science 340: 1451-1455

  • DOI: 10.1126/science.1237908
  • Primary Citation of Related Structures:  4K7D

  • PubMed Abstract: 
  • Mutations in the PARK2 (parkin) gene are responsible for an autosomal recessive form of Parkinson's disease. The parkin protein is a RING-in-between-RING E3 ubiquitin ligase that exhibits low basal activity. We describe the crystal structure of full- ...

    Mutations in the PARK2 (parkin) gene are responsible for an autosomal recessive form of Parkinson's disease. The parkin protein is a RING-in-between-RING E3 ubiquitin ligase that exhibits low basal activity. We describe the crystal structure of full-length rat parkin. The structure shows parkin in an autoinhibited state and provides insight into how it is activated. RING0 occludes the ubiquitin acceptor site Cys(431) in RING2, whereas a repressor element of parkin binds RING1 and blocks its E2-binding site. Mutations that disrupted these inhibitory interactions activated parkin both in vitro and in cells. Parkin is neuroprotective, and these findings may provide a structural and mechanistic framework for enhancing parkin activity.


    Organizational Affiliation

    McGill Parkinson Program, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, Québec, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase parkin
A, B, C, D, E, F, G, H, I, J, K, L
470Rattus norvegicusGene Names: Park2 (Prkn)
EC: 6.3.2.-
Find proteins for Q9JK66 (Rattus norvegicus)
Go to UniProtKB:  Q9JK66
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.499 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.307 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 208.598α = 90.00
b = 277.439β = 90.00
c = 125.891γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
SCALEPACKdata scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-05-22
    Type: Database references
  • Version 1.2: 2013-07-10
    Type: Database references