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- PDB-9eij: Import stalled PINK1 TOM complex, extended TOM20 helix class -

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Basic information

Entry
Database: PDB / ID: 9eij
TitleImport stalled PINK1 TOM complex, extended TOM20 helix class
Components
  • (Mitochondrial import receptor subunit ...) x 6
  • Non-selective voltage-gated ion channel VDAC2
  • Serine/threonine-protein kinase PINK1, mitochondrial
KeywordsTRANSLOCASE / PINK1 / TOM complex / VDAC
Function / homology
Function and homology information


positive regulation of free ubiquitin chain polymerization / positive regulation of synaptic transmission, dopaminergic / tRNA import into mitochondrion / positive regulation of cristae formation / voltage-gated monoatomic anion channel activity / TOM complex / mitochondrial transmembrane transport / mitochondrial outer membrane permeabilization / : / Mitochondrial calcium ion transport ...positive regulation of free ubiquitin chain polymerization / positive regulation of synaptic transmission, dopaminergic / tRNA import into mitochondrion / positive regulation of cristae formation / voltage-gated monoatomic anion channel activity / TOM complex / mitochondrial transmembrane transport / mitochondrial outer membrane permeabilization / : / Mitochondrial calcium ion transport / mitochondrion to lysosome vesicle-mediated transport / maintenance of protein location in mitochondrion / mitochondrion targeting sequence binding / : / mitochondrial outer membrane translocase complex / cellular response to hydrogen sulfide / protein kinase B binding / Lewy body / regulation of autophagy of mitochondrion / phospholipid scramblase activity / regulation of synaptic vesicle transport / ceramide binding / TORC2 signaling / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / positive regulation of mitochondrial electron transport, NADH to ubiquinone / regulation of oxidative phosphorylation / regulation of hydrogen peroxide metabolic process / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / C3HC4-type RING finger domain binding / protein-transporting ATPase activity / dopamine secretion / migrasome / regulation of cellular response to oxidative stress / negative regulation of autophagosome assembly / voltage-gated monoatomic ion channel activity / binding of sperm to zona pellucida / positive regulation of dopamine secretion / autophagy of mitochondrion / oxysterol binding / phosphatidylcholine binding / positive regulation of type 2 mitophagy / Mitochondrial protein import / cellular response to toxic substance / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrion organization / monoatomic anion transport / negative regulation of JNK cascade / regulation of reactive oxygen species metabolic process / : / peptidase activator activity / phospholipid translocation / : / cholesterol binding / astrocyte projection / positive regulation of ubiquitin-protein transferase activity / positive regulation of mitochondrial fission / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of macroautophagy / porin activity / negative regulation of mitophagy / FOXO-mediated transcription of cell death genes / pore complex / protein import into mitochondrial matrix / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of release of cytochrome c from mitochondria / positive regulation of ATP biosynthetic process / negative regulation of reactive oxygen species metabolic process / hemopoiesis / mitochondrial nucleoid / positive regulation of macroautophagy / regulation of protein ubiquitination / protein transmembrane transporter activity / negative regulation of mitochondrial fission / regulation of protein-containing complex assembly / mitophagy / regulation of proteasomal protein catabolic process / monoatomic ion transport / acrosomal vesicle / positive regulation of protein ubiquitination / response to ischemia / positive regulation of translation / cell periphery / PINK1-PRKN Mediated Mitophagy / regulation of mitochondrial membrane potential / respiratory electron transport chain / mitochondrion organization / macroautophagy / regulation of protein stability / mitochondrial intermembrane space / mitochondrial membrane / kinase binding / kinase activity / unfolded protein binding / sperm midpiece / growth cone / cell body / response to oxidative stress / cellular response to oxidative stress
Similarity search - Function
PINK1, protein kinase domain / Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / Protein import receptor MAS20, metazoan / Protein import receptor MAS20 / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor ...PINK1, protein kinase domain / Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / Protein import receptor MAS20, metazoan / Protein import receptor MAS20 / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / : / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Mitochondrial import receptor subunit TOM40 homolog / Non-selective voltage-gated ion channel VDAC2 / Mitochondrial import receptor subunit TOM20 homolog / Mitochondrial import receptor subunit TOM5 homolog / Mitochondrial import receptor subunit TOM6 homolog / Serine/threonine-protein kinase PINK1, mitochondrial / Mitochondrial import receptor subunit TOM22 homolog / Mitochondrial import receptor subunit TOM7 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKirk, N.S. / Glukhova, A. / Callegari, S. / Komander, D.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1178122 Australia
Other private Australia
CitationJournal: Science / Year: 2025
Title: Structure of human PINK1 at a mitochondrial TOM-VDAC array.
Authors: Sylvie Callegari / Nicholas S Kirk / Zhong Yan Gan / Toby Dite / Simon A Cobbold / Andrew Leis / Laura F Dagley / Alisa Glukhova / David Komander /
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 ...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-angstrom resolution cryo-electron microscopy structure of dimeric human PINK1 stabilized at an endogenous array of mitochondrial translocase of the outer membrane (TOM) and voltage-dependent anion channel (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.
History
DepositionNov 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references / Structure summary
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Revision 1.1Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Mitochondrial import receptor subunit TOM20 homolog
E: Non-selective voltage-gated ion channel VDAC2
F: Non-selective voltage-gated ion channel VDAC2
I: Mitochondrial import receptor subunit TOM40 homolog
J: Mitochondrial import receptor subunit TOM40 homolog
K: Mitochondrial import receptor subunit TOM5 homolog
L: Mitochondrial import receptor subunit TOM5 homolog
N: Mitochondrial import receptor subunit TOM7 homolog
P: Mitochondrial import receptor subunit TOM6 homolog
R: Mitochondrial import receptor subunit TOM22 homolog
T: Mitochondrial import receptor subunit TOM22 homolog
V: Mitochondrial import receptor subunit TOM6 homolog
X: Mitochondrial import receptor subunit TOM7 homolog
Z: Mitochondrial import receptor subunit TOM5 homolog
B: Serine/threonine-protein kinase PINK1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,77724
Polymers298,66615
Non-polymers7,1119
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Mitochondrial import receptor subunit ... , 6 types, 12 molecules DIJKLZNXPVRT

#1: Protein Mitochondrial import receptor subunit TOM20 homolog / Mitochondrial 20 kDa outer membrane protein / Outer mitochondrial membrane receptor Tom20


Mass: 16319.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293 / References: UniProt: Q15388
#3: Protein Mitochondrial import receptor subunit TOM40 homolog / Protein Haymaker / Translocase of outer membrane 40 kDa subunit homolog / p38.5


Mass: 37926.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293 / References: UniProt: O96008
#4: Protein Mitochondrial import receptor subunit TOM5 homolog


Mass: 6045.318 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293 / References: UniProt: Q8N4H5
#5: Protein Mitochondrial import receptor subunit TOM7 homolog / Translocase of outer membrane 7 kDa subunit homolog


Mass: 6256.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293 / References: UniProt: Q9P0U1
#6: Protein Mitochondrial import receptor subunit TOM6 homolog / Overexpressed breast tumor protein / Translocase of outer membrane 6 kDa subunit homolog


Mass: 8007.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293 / References: UniProt: Q96B49
#7: Protein Mitochondrial import receptor subunit TOM22 homolog / hTom22 / 1C9-2 / Translocase of outer membrane 22 kDa subunit homolog


Mass: 15532.528 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293 / References: UniProt: Q9NS69

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Protein , 2 types, 3 molecules EFB

#2: Protein Non-selective voltage-gated ion channel VDAC2 / VDAC-2 / hVDAC2 / Outer mitochondrial membrane protein porin 2


Mass: 31600.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293 / References: UniProt: P45880
#8: Protein Serine/threonine-protein kinase PINK1, mitochondrial / BRPK / PTEN-induced putative kinase protein 1


Mass: 65561.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PINK1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
References: UniProt: Q9BXM7, non-specific serine/threonine protein kinase

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Non-polymers , 1 types, 9 molecules

#9: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of VDAC, TOM core and PINK1 / Type: COMPLEX / Entity ID: #8, #1-#7 / Source: RECOMBINANT
Molecular weightValue: 0.75 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: EXPI293
Buffer solutionpH: 7.4
SpecimenConc.: 4.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K / Details: Blot force 10 for 2 s.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.34 sec. / Electron dose: 52.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 16992

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Processing

EM software
IDNameVersionCategoryDetailsFitting-ID
1cryoSPARC4.5particle selection
3EPU3image acquisitionAFIS - faster acquisition
5cryoSPARC4.5CTF correction
8ISOLDE7model fitting1
10PHENIX1.21.1_5286model refinement1
13ISOLDE7model fitting2
14PHENIX1.21.1_5286model refinement2
CTF correctionDetails: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5700000 / Details: Picked using low resolution templates
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 165000 / Symmetry type: POINT
Atomic model building
IDProtocolSpace
1FLEXIBLE FITREAL
2FLEXIBLE FITREAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17CP9

7cp9

17CP91PDBexperimental model
22AlphaFoldin silico model
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217305
ELECTRON MICROSCOPYf_angle_d0.64523304
ELECTRON MICROSCOPYf_dihedral_angle_d13.6936609
ELECTRON MICROSCOPYf_chiral_restr0.0422559
ELECTRON MICROSCOPYf_plane_restr0.0062940

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