6HUE

ParkinS65N

• PDB DOI:  https://doi.org/10.2210/pdb6HUE/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-10-07 Released: 2018-10-17 
• Deposition Author(s): McWilliams, T.G., Barini, E., Pohjolan-Pirhonen, R., Brooks, S.P., Singh, F., Burel, S., Balk, K., Kumar, A., Montava-Garriga, L., Prescott, A.R., Hassoun, S.M., Mouton-Liger, F., Ball, G., Hills, R., Knebel, A., Ulusoy, A., Di Monte, D.A., Tamjar, J., Antico, O., Fears, K., Smith, L., Brambilla, R., Palin, E., Valori, M., Eerola-Rautio, J., Tienari, P., Corti, O., Dunnett, S.B., Ganley, I.G., Suomalainen, A., Muqit, M.M.K.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.255 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 

Literature

Phosphorylation of Parkin at serine 65 is essential for its activation in vivo .

McWilliams, T.G., Barini, E., Pohjolan-Pirhonen, R., Brooks, S.P., Singh, F., Burel, S., Balk, K., Kumar, A., Montava-Garriga, L., Prescott, A.R., Hassoun, S.M., Mouton-Liger, F., Ball, G., Hills, R., Knebel, A., Ulusoy, A., Di Monte, D.A., Tamjar, J., Antico, O., Fears, K., Smith, L., Brambilla, R., Palin, E., Valori, M., Eerola-Rautio, J., Tienari, P., Corti, O., Dunnett, S.B., Ganley, I.G., Suomalainen, A., Muqit, M.M.K.

(2018) Open Biol 8

• PubMed: 30404819 
• DOI: https://doi.org/10.1098/rsob.180108
• Primary Citation of Related Structures:  
  6HUE


• PubMed Abstract: 
  

Mutations in PINK1 and Parkin result in autosomal recessive Parkinson's disease (PD). Cell culture and in vitro studies have elaborated the PINK1-dependent regulation of Parkin and defined how this dyad orchestrates the elimination of damaged mitochondria via mitophagy. PINK1 phosphorylates ubiquitin at serine 65 (Ser65) and Parkin at an equivalent Ser65 residue located within its N-terminal ubiquitin-like domain, resulting in activation; however, the physiological significance of Parkin Ser65 phosphorylation in vivo in mammals remains unknown. To address this, we generated a Parkin Ser65Ala (S65A) knock-in mouse model. We observe endogenous Parkin Ser65 phosphorylation and activation in mature primary neurons following mitochondrial depolarization and reveal this is disrupted in Parkin ^S65A/S65A neurons. Phenotypically, Parkin ^S65A/S65A mice exhibit selective motor dysfunction in the absence of any overt neurodegeneration or alterations in nigrostriatal mitophagy. The clinical relevance of our findings is substantiated by the discovery of homozygous PARKIN ( PARK2 ) p.S65N mutations in two unrelated patients with PD. Moreover, biochemical and structural analysis demonstrates that the Parkin ^S65N/S65N mutant is pathogenic and cannot be activated by PINK1. Our findings highlight the central role of Parkin Ser65 phosphorylation in health and disease.

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Organizational Affiliation: 

School of Medicine, University of Dundee, Dundee DD1 9SY, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 92.98 kDa 
• Atom Count: 6,333 
• Modelled Residue Count: 760 
• Deposited Residue Count: 810 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase parkin	A, B	405	Homo sapiens	Mutation(s): 1  Gene Names: PRKN, PARK2 EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for O60260 (Homo sapiens) Explore O60260  Go to UniProtKB:  O60260
PHAROS:  O60260

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	K [auth A], W [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	L [auth A], M [auth A], X [auth B], Y [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	N [auth A], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.255 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.431	α = 90
b = 66.87	β = 90
c = 206.69	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): McWilliams, T.G., Barini, E., Pohjolan-Pirhonen, R., Brooks, S.P., Singh, F., Burel, S., Balk, K., Kumar, A., Montava-Garriga, L., Prescott, A.R., Hassoun, S.M., Mouton-Liger, F., Ball, G., Hills, R., Knebel, A., Ulusoy, A., Di Monte, D.A., Tamjar, J., Antico, O., Fears, K., Smith, L., Brambilla, R., Palin, E., Valori, M., Eerola-Rautio, J., Tienari, P., Corti, O., Dunnett, S.B., Ganley, I.G., Suomalainen, A., Muqit, M.M.K.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	101022/Z/13/Z

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2018-11-21
  Changes: Data collection, Database references
• Version 1.2: 2020-09-30
  Changes: Database references