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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


negative regulation of protein polymerization / positive regulation of synaptic transmission, dopaminergic / positive regulation of free ubiquitin chain polymerization / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / tRNA import into mitochondrion / positive regulation of cristae formation / TOM complex / TORC2 signaling / regulation of protein targeting to mitochondrion / voltage-gated monoatomic anion channel activity ...negative regulation of protein polymerization / positive regulation of synaptic transmission, dopaminergic / positive regulation of free ubiquitin chain polymerization / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / tRNA import into mitochondrion / positive regulation of cristae formation / TOM complex / TORC2 signaling / regulation of protein targeting to mitochondrion / voltage-gated monoatomic anion channel activity / mitochondrial transmembrane transport / mitochondrial outer membrane permeabilization / : / mitochondrion targeting sequence binding / mitochondrion to lysosome vesicle-mediated transport / Mitochondrial calcium ion transport / maintenance of protein location in mitochondrion / cellular response to hydrogen sulfide / mitochondrial outer membrane translocase complex / Lewy body / protein kinase B binding / establishment of protein localization to mitochondrion / migrasome / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / phospholipid scramblase activity / positive regulation of type 2 mitophagy / regulation of synaptic vesicle transport / regulation of autophagy of mitochondrion / mitochondria-associated endoplasmic reticulum membrane contact site / protein import into mitochondrial matrix / ceramide binding / positive regulation of mitochondrial electron transport, NADH to ubiquinone / regulation of hydrogen peroxide metabolic process / peptidase activator activity / C3HC4-type RING finger domain binding / voltage-gated monoatomic ion channel activity / protein-transporting ATPase activity / regulation of cellular response to oxidative stress / dopamine secretion / positive regulation of dopamine secretion / negative regulation of autophagosome assembly / peptidyl-serine autophosphorylation / cellular response to toxic substance / binding of sperm to zona pellucida / Mitochondrial protein import / regulation of oxidative phosphorylation / astrocyte projection / phosphatidylcholine binding / protein targeting to mitochondrion / negative regulation of JNK cascade / oxysterol binding / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / TORC2 complex binding / monoatomic anion transport / regulation of mitochondrion organization / negative regulation of mitophagy / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of reactive oxygen species metabolic process / positive regulation of ubiquitin-protein transferase activity / autophagy of mitochondrion / positive regulation of protein targeting to mitochondrion / phospholipid translocation / positive regulation of ATP biosynthetic process / cholesterol binding / protein insertion into mitochondrial outer membrane / negative regulation of macroautophagy / positive regulation of mitochondrial fission / porin activity / pore complex / FOXO-mediated transcription of cell death genes / positive regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / mitochondrial nucleoid / positive regulation of macroautophagy / hemopoiesis / regulation of protein ubiquitination / protein transmembrane transporter activity / regulation of protein-containing complex assembly / negative regulation of mitochondrial fission / negative regulation of reactive oxygen species metabolic process / mitophagy / eukaryotic translation initiation factor 2alpha kinase activity / histone H4S1 kinase activity / histone H2AS121 kinase activity / histone H3S57 kinase activity / histone H2BS14 kinase activity / histone H3S28 kinase activity / regulation of proteasomal protein catabolic process / monoatomic ion transport / histone H2BS36 kinase activity / ribosomal protein S6 kinase activity / histone H3T6 kinase activity / activation of protein kinase B activity / histone H2AT120 kinase activity / histone H3T3 kinase activity / Rho-dependent protein serine/threonine kinase activity / 3-phosphoinositide-dependent protein kinase activity / histone H3T45 kinase activity / sperm midpiece / DNA-dependent protein kinase activity
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 / Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type ...PINK1, protein kinase domain / Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / : / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / 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.
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: Callegari, S. / Kirk, N.S. / Gan, Z.Y. / Cobbold, S.A. / Dite, T. / Leis, A. / Dagley, L.F. / Glukhova, A. / Komander, D.
History
DepositionNov 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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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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