4K7D

Crystal Structure of Parkin C-terminal RING domains

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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: https://doi.org/10.1126/science.1237908
  • Primary Citation of Related Structures:  
    4K7D, 4K95

  • 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-length rat parkin ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase parkinA, B, C330Rattus norvegicusMutation(s): 0 
Gene Names: Park2, Prkn
EC: 6.3.2 (PDB Primary Data), 2.3.2.31 (UniProt)
UniProt
Find proteins for Q9JK66 (Rattus norvegicus)
Explore Q9JK66 
Go to UniProtKB:  Q9JK66
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JK66
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI
Download Ideal Coordinates CCD File 
DA [auth C],
L [auth A],
U [auth B]		MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
CA [auth C],
D [auth A],
E [auth A],
AA [auth C],
BA [auth C],
CA [auth C],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
EA [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.7α = 90
b = 106.625β = 90
c = 154.216γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MxDCdata collection
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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