Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 52532.38 
• Atom Count: 3080 
• Residue Count: 465 
• Unique protein chains: 2

6GLC

Structure of phospho-Parkin bound to phospho-ubiquitin

• DOI: 10.2210/pdb6GLC/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2018-05-23 Released: 2018-06-13 
• Deposition Author(s): Gladkova, C., Maslen, S.L., Skehel, J.M., Komander, D.
• Funding Organization(s): Medical Research Council (United Kingdom); European Research Council; Michael J. Fox Foundation 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.205 
• R-Value Work: 0.180 

Literature

Mechanism of parkin activation by PINK1.

Gladkova, C., Maslen, S.L., Skehel, J.M., Komander, D.

(2018) Nature 559: 410-414

• PubMed: 29995846 
• DOI: 10.1038/s41586-018-0224-x


• PubMed Abstract: 
  

Mutations in the E3 ubiquitin ligase parkin (PARK2, also known as PRKN) and the protein kinase PINK1 (also known as PARK6) are linked to autosomal-recessive juvenile parkinsonism (AR-JP) ^1,2 ; at the cellular level, these mutations cause defects in mitophagy, the process that organizes the destruction of damaged mitochondria ^3,4 . Parkin is autoinhibited, and requires activation by PINK1, which phosphorylates Ser65 in ubiquitin and in the parkin ubiquitin-like (Ubl) domain. Parkin binds phospho-ubiquitin, which enables efficient parkin phosphorylation; however, the enzyme remains autoinhibited with an inaccessible active site ^5,6 . It is unclear how phosphorylation of parkin activates the molecule. Here we follow the activation of full-length human parkin by hydrogen-deuterium exchange mass spectrometry, and reveal large-scale domain rearrangement in the activation process, during which the phospho-Ubl rebinds to the parkin core and releases the catalytic RING2 domain. A 1.8 Å crystal structure of phosphorylated human parkin reveals the binding site of the phospho-Ubl on the unique parkin domain (UPD), involving a phosphate-binding pocket lined by AR-JP mutations. Notably, a conserved linker region between Ubl and the UPD acts as an activating element (ACT) that contributes to RING2 release by mimicking RING2 interactions on the UPD, explaining further AR-JP mutations. Our data show how autoinhibition in parkin is resolved, and suggest a mechanism for how parkin ubiquitinates its substrates via an untethered RING2 domain. These findings open new avenues for the design of parkin activators for clinical use.

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Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Medical Research Council Laboratory of Molecular Biology, Cambridge, UK. [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
E3 ubiquitin-protein ligase parkin	A	389	Homo sapiens	Mutation(s): 1  Gene Names: PRKN (PARK2) EC: 2.3.2.31
Find proteins for O60260 (Homo sapiens) Go to Gene View: PRKN Go to UniProtKB:  O60260

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Polyubiquitin-B	B	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MPD	A	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
3CN	B	NON-POLYMER	C3 H9 N		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.205 
• R-Value Work: 0.180 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 83.931	α = 90.00
b = 83.931	β = 90.00
c = 105.119	γ = 120.00

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
DIALS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-05-23 
• Released Date: 2018-06-13 
• Deposition Author(s): Gladkova, C., Maslen, S.L., Skehel, J.M., Komander, D.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	U105192732
European Research Council	United Kingdom	309756
European Research Council	United Kingdom	724804
Michael J. Fox Foundation	United Kingdom	--

Revision History 

• Version 1.0: 2018-06-13
  Type: Initial release
• Version 1.1: 2018-07-18
  Type: Data collection, Database references
• Version 1.2: 2018-08-01
  Type: Data collection, Database references