7T3X

Structure of unphosphorylated Pediculus humanus (Ph) PINK1 D334A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.53 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Activation mechanism of PINK1.

Gan, Z.Y.Callegari, S.Cobbold, S.A.Cotton, T.R.Mlodzianoski, M.J.Schubert, A.F.Geoghegan, N.D.Rogers, K.L.Leis, A.Dewson, G.Glukhova, A.Komander, D.

(2022) Nature 602: 328-335

  • DOI: https://doi.org/10.1038/s41586-021-04340-2
  • Primary Citation of Related Structures:  
    7T3X, 7T4K, 7T4L, 7T4M, 7T4N

  • PubMed Abstract: 

    Mutations in the protein kinase PINK1 lead to defects in mitophagy and cause autosomal recessive early onset Parkinson's disease 1,2 . PINK1 has many unique features that enable it to phosphorylate ubiquitin and the ubiquitin-like domain of Parkin 3-9 . Structural analysis of PINK1 from diverse insect species 10-12 with and without ubiquitin provided snapshots of distinct structural states yet did not explain how PINK1 is activated. Here we elucidate the activation mechanism of PINK1 using crystallography and cryo-electron microscopy (cryo-EM). A crystal structure of unphosphorylated Pediculus humanus corporis (Ph; human body louse) PINK1 resolves an N-terminal helix, revealing the orientation of unphosphorylated yet active PINK1 on the mitochondria. We further provide a cryo-EM structure of a symmetric PhPINK1 dimer trapped during the process of trans-autophosphorylation, as well as a cryo-EM structure of phosphorylated PhPINK1 undergoing a conformational change to an active ubiquitin kinase state. Structures and phosphorylation studies further identify a role for regulatory PINK1 oxidation. Together, our research delineates the complete activation mechanism of PINK1, illuminates how PINK1 interacts with the mitochondrial outer membrane and reveals how PINK1 activity may be modulated by mitochondrial reactive oxygen species.


  • Organizational Affiliation

    Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PINK1463Pediculus humanus corporisMutation(s): 1 
Gene Names: 8239562Phum_PHUM577390
EC: 2.7.11.1
UniProt
Find proteins for E0W1I1 (Pediculus humanus subsp. corporis)
Explore E0W1I1 
Go to UniProtKB:  E0W1I1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0W1I1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.53 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.118α = 90
b = 116.118β = 90
c = 70.565γ = 120
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)United States--
Michael J. Fox FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2022-01-12
    Changes: Database references
  • Version 1.2: 2022-02-23
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description