Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 91.01 kDa 
• Atom Count: 5627 
• Residue Count: 765 
• Unique protein chains: 2

5CAW

Structure of Pediculus humanus Parkin bound to phospho-ubiquitin

• DOI: 10.2210/pdb5CAW/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Pediculus humanus corporis, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-06-30 Released: 2015-07-22 
• Deposition Author(s): Wauer, T., Komander, D.
• Funding Organization(s): Medical Research Council (United Kingdom), European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.260 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 

Literature

Mechanism of phospho-ubiquitin-induced PARKIN activation.

Wauer, T., Simicek, M., Schubert, A., Komander, D.

(2015) Nature 524: 370-374

• PubMed: 26161729 
• DOI: 10.1038/nature14879
• Primary Citation of Related Structures:  
  5CAW, 5C9V


• PubMed Abstract: 
  

The E3 ubiquitin ligase PARKIN (encoded by PARK2) and the protein kinase PINK1 (encoded by PARK6) are mutated in autosomal-recessive juvenile Parkinsonism (AR-JP) and work together in the disposal of damaged mitochondria by mitophagy. PINK1 is stabilized on the outside of depolarized mitochondria and phosphorylates polyubiquitin as well as the PARKIN ubiquitin-like (Ubl) domain. These phosphorylation events lead to PARKIN recruitment to mitochondria, and activation by an unknown allosteric mechanism. Here we present the crystal structure of Pediculus humanus PARKIN in complex with Ser65-phosphorylated ubiquitin (phosphoUb), revealing the molecular basis for PARKIN recruitment and activation. The phosphoUb binding site on PARKIN comprises a conserved phosphate pocket and harbours residues mutated in patients with AR-JP. PhosphoUb binding leads to straightening of a helix in the RING1 domain, and the resulting conformational changes release the Ubl domain from the PARKIN core; this activates PARKIN. Moreover, phosphoUb-mediated Ubl release enhances Ubl phosphorylation by PINK1, leading to conformational changes within the Ubl domain and stabilization of an open, active conformation of PARKIN. We redefine the role of the Ubl domain not only as an inhibitory but also as an activating element that is restrained in inactive PARKIN and released by phosphoUb. Our work opens up new avenues to identify small-molecule PARKIN activators.

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Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase parkin	A, C	321	Pediculus humanus corporis	Mutation(s): 0  Gene Names: Phum_PHUM233570, 8230172 EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for E0VIU9 (Pediculus humanus subsp. corporis) Explore E0VIU9  Go to UniProtKB:  E0VIU9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B, D	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, C, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	A, C	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B,D	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.260 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.17	α = 90
b = 44.12	β = 92.55
c = 204.531	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-06-30 
• Released Date: 2015-07-22 
Deposition Author(s): Wauer, T., 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

Revision History 

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2015-07-29
  Changes: Database references
• Version 1.2: 2015-08-26
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Advisory, Author supporting evidence, Derived calculations