[English] 日本語
Yorodumi
- PDB-9eii: Import stalled PINK1 TOM complex, symmetry expanded -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9eii
TitleImport stalled PINK1 TOM complex, symmetry expanded
Components
  • (Mitochondrial import receptor subunit ...) x 6
  • Serine/threonine-protein kinase PINK1, mitochondrial
  • Voltage-dependent anion-selective channel protein 2
KeywordsTRANSLOCASE / PINK1 / TOM complex / VDAC
Function / homology
Function and homology information


positive regulation of synaptic transmission, dopaminergic / positive regulation of free ubiquitin chain polymerization / positive regulation of cristae formation / tRNA import into mitochondrion / TOM complex / voltage-gated monoatomic anion channel activity / mitochondrial transmembrane transport / regulation of protein targeting to mitochondrion / mitochondrial outer membrane permeabilization / mitochondrion to lysosome vesicle-mediated transport ...positive regulation of synaptic transmission, dopaminergic / positive regulation of free ubiquitin chain polymerization / positive regulation of cristae formation / tRNA import into mitochondrion / TOM complex / voltage-gated monoatomic anion channel activity / mitochondrial transmembrane transport / regulation of protein targeting to mitochondrion / mitochondrial outer membrane permeabilization / mitochondrion to lysosome vesicle-mediated transport / Mitochondrial calcium ion transport / maintenance of protein location in mitochondrion / mitochondrion targeting sequence binding / establishment of protein localization to mitochondrion / protein kinase B binding / cellular response to hydrogen sulfide / mitochondrial outer membrane translocase complex / Lewy body / phospholipid scramblase activity / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / TORC2 signaling / regulation of autophagy of mitochondrion / regulation of synaptic vesicle transport / ceramide binding / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mitochondria-associated endoplasmic reticulum membrane contact site / regulation of hydrogen peroxide metabolic process / regulation of oxidative phosphorylation / migrasome / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / protein import into mitochondrial matrix / C3HC4-type RING finger domain binding / peptidase activator activity / regulation of cellular response to oxidative stress / dopamine secretion / protein-transporting ATPase activity / voltage-gated monoatomic ion channel activity / positive regulation of dopamine secretion / negative regulation of autophagosome assembly / binding of sperm to zona pellucida / autophagy of mitochondrion / phosphatidylcholine binding / positive regulation of type 2 mitophagy / astrocyte projection / oxysterol binding / Mitochondrial protein import / cellular response to toxic substance / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / monoatomic anion transport / regulation of mitochondrion organization / negative regulation of JNK cascade / positive regulation of ubiquitin-protein transferase activity / protein targeting to mitochondrion / positive regulation of protein targeting to mitochondrion / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of reactive oxygen species metabolic process / phospholipid translocation / cholesterol binding / negative regulation of macroautophagy / positive regulation of mitochondrial fission / porin activity / negative regulation of mitophagy / pore complex / FOXO-mediated transcription of cell death genes / protein insertion into mitochondrial outer membrane / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of release of cytochrome c from mitochondria / positive regulation of ATP biosynthetic process / hemopoiesis / mitochondrial nucleoid / negative regulation of reactive oxygen species metabolic process / positive regulation of macroautophagy / protein transmembrane transporter activity / regulation of protein ubiquitination / negative regulation of mitochondrial fission / regulation of protein-containing complex assembly / mitophagy / monoatomic ion transport / sperm midpiece / regulation of proteasomal protein catabolic process / acrosomal vesicle / positive regulation of translation / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / response to ischemia / cell periphery / respiratory electron transport chain / regulation of mitochondrial membrane potential / mitochondrion organization / macroautophagy / mitochondrial membrane / regulation of protein stability / mitochondrial intermembrane space / kinase binding / kinase activity / unfolded protein binding / cell body / growth cone / cellular response to oxidative stress / protease binding
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: 2.75 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
Category: audit_author / citation ...audit_author / citation / citation_author / em_admin / em_author_list
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.1Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Category: citation / citation_author ...citation / citation_author / em_admin / em_author_list
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.2Apr 30, 2025Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / em_admin / em_author_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Serine/threonine-protein kinase PINK1, mitochondrial
D: Mitochondrial import receptor subunit TOM20 homolog
F: Voltage-dependent anion-selective channel protein 2
I: Mitochondrial import receptor subunit TOM40 homolog
J: Mitochondrial import receptor subunit TOM40 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,13222
Polymers261,02013
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

-
Components

-
Protein , 2 types, 2 molecules BF

#1: 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
#3: Protein Voltage-dependent anion-selective channel protein 2 / VDAC-2 / hVDAC2 / Outer mitochondrial membrane protein porin 2


Mass: 31600.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293 / References: UniProt: P45880

-
Mitochondrial import receptor subunit ... , 6 types, 11 molecules DIJLZNXPVRT

#2: 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
#4: 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
#5: Protein Mitochondrial import receptor subunit TOM5 homolog


Mass: 6045.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293 / References: UniProt: Q8N4H5
#6: 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
#7: 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
#8: 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

-
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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Complex of VDAC, TOM core and PINK1 / Type: COMPLEX / Entity ID: #1-#8 / 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.

-
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

-
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: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 791000 / 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: 2.75 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214737
ELECTRON MICROSCOPYf_angle_d0.67319839
ELECTRON MICROSCOPYf_dihedral_angle_d13.9245684
ELECTRON MICROSCOPYf_chiral_restr0.0422167
ELECTRON MICROSCOPYf_plane_restr0.0062499

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more