7T4N

Structure of dimeric unphosphorylated Pediculus humanus (Ph) PINK1 D357A mutant


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 PINK1, putative
A, B
463Pediculus 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: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2-4158

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Author supporting evidence, Data collection, Refinement description