9EII | pdb_00009eii

Import stalled PINK1 TOM complex, symmetry expanded


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of human PINK1 at a mitochondrial TOM-VDAC array.

Callegari, S.Kirk, N.S.Gan, Z.Y.Dite, T.Cobbold, S.A.Leis, A.Dagley, L.F.Glukhova, A.Komander, D.

(2025) Science : eadu6445-eadu6445

  • DOI: https://doi.org/10.1126/science.adu6445
  • Primary Citation of Related Structures:  
    9EIH, 9EII, 9EIJ

  • PubMed Abstract: 

    Mutations in the ubiquitin kinase PINK1 cause early onset Parkinson's Disease, but how PINK1 is stabilized at depolarized mitochondrial translocase complexes has remained poorly understood. We determined a 3.1-Å resolution cryo-electron microscopy structure of dimeric human PINK1 stabilized at an endogenous array of mitochondrial TOM and VDAC complexes. Symmetric arrangement of two TOM core complexes around a central VDAC2 dimer is facilitated by TOM5 and TOM20, both of which also bind PINK1 kinase C-lobes. PINK1 enters mitochondria through the proximal TOM40 barrel of the TOM core complex, guided by TOM7 and TOM22. Our structure explains how human PINK1 is stabilized at the TOM complex and regulated by oxidation, uncovers a previously unknown TOM-VDAC assembly, and reveals how a physiological substrate traverses TOM40 during translocation.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PINK1, mitochondrialA [auth B]603Homo sapiensMutation(s): 0 
Gene Names: PINK1
EC: 2.7.11.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXM7 (Homo sapiens)
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Go to UniProtKB:  Q9BXM7
PHAROS:  Q9BXM7
GTEx:  ENSG00000158828 
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UniProt GroupQ9BXM7
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM20 homologB [auth D]145Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q15388 (Homo sapiens)
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PHAROS:  Q15388
GTEx:  ENSG00000173726 
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UniProt GroupQ15388
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent anion-selective channel protein 2C [auth F]294Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P45880 (Homo sapiens)
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PHAROS:  P45880
GTEx:  ENSG00000165637 
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UniProt GroupP45880
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM40 homologD [auth I],
E [auth J]
361Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O96008 (Homo sapiens)
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PHAROS:  O96008
GTEx:  ENSG00000130204 
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UniProt GroupO96008
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM5 homologF [auth L],
M [auth Z]
51Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000175768 
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UniProt GroupQ8N4H5
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM7 homologG [auth N],
L [auth X]
55Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9P0U1 (Homo sapiens)
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PHAROS:  Q9P0U1
GTEx:  ENSG00000196683 
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UniProt GroupQ9P0U1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM6 homologH [auth P],
K [auth V]
74Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q96B49 (Homo sapiens)
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PHAROS:  Q96B49
GTEx:  ENSG00000214736 
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UniProt GroupQ96B49
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial import receptor subunit TOM22 homologI [auth R],
J [auth T]
142Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9NS69 (Homo sapiens)
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PHAROS:  Q9NS69
GTEx:  ENSG00000100216 
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UniProt GroupQ9NS69
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1

Download Ideal Coordinates CCD File 
N [auth F]
O [auth I]
P [auth I]
Q [auth I]
R [auth J]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT1178122
Other privateAustralia--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Data collection, Database references, Structure summary