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- PDB-9wv3: Human TOM complex with substrate Tim22-GGC1-sfGFP -

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Basic information

Entry
Database: PDB / ID: 9wv3
TitleHuman TOM complex with substrate Tim22-GGC1-sfGFP
Components
  • (Mitochondrial import receptor subunit ...) x 5
  • Mitochondrial GTP/GDP carrier protein 1
KeywordsTRANSLOCASE / Mitochondria / Protein translocation
Function / homology
Function and homology information


guanine nucleotide transport / : / guanine nucleotide transmembrane transporter activity / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of type 2 mitophagy / Mitochondrial protein import / : ...guanine nucleotide transport / : / guanine nucleotide transmembrane transporter activity / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of type 2 mitophagy / Mitochondrial protein import / : / : / porin activity / pore complex / protein import into mitochondrial matrix / transmembrane protein transporter activity / monoatomic ion transport / PINK1-PRKN Mediated Mitophagy / regulation of protein stability / intracellular protein transport / transmembrane transport / protein transport / intracellular iron ion homeostasis / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrion / membrane
Similarity search - Function
: / Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile. / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase ...: / Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile. / 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
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / HEXADECANE / Mitochondrial import receptor subunit TOM40 homolog / Mitochondrial GTP/GDP carrier protein 1 / Mitochondrial import receptor subunit TOM5 homolog / Mitochondrial import receptor subunit TOM6 homolog / Mitochondrial import receptor subunit TOM22 homolog / Mitochondrial import receptor subunit TOM7 homolog
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsLiu, X.L. / Cai, H.J. / Li, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271269 China
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Direct coupling of human TOM and TIM22 complexes drives mitochondrial carrier import.
Authors: Xiaolong Liu / Hongjun Cai / Hao Wang / Xueyin Zhou / Yutong Zhang / Shuai Liu / Jiajun Zhu / Long Li /
Abstract: Metabolite carriers that control essential metabolite transport are imported into mitochondria through the TOM and TIM22 complexes. How TOM and TIM22 coordinate in human mitochondria has remained ...Metabolite carriers that control essential metabolite transport are imported into mitochondria through the TOM and TIM22 complexes. How TOM and TIM22 coordinate in human mitochondria has remained largely unknown. Here we show that human TOM and TIM22 assemble into a supercomplex that seamlessly couples carrier translocation across the outer and inner membranes, unlike in yeast where the two complexes appear to function separately. Cryo-electron microscopy structures of the human TOM-TIM22 supercomplex reveal unpaired carrier transmembrane segments traversing the TOM channel along a hydrophobic path and exiting through an unexpected lateral groove outside the channel. The membrane-bound small Tim subunits provide the substrate entry site for TIM22, while a membrane-exposed groove of TIM22 serves as the exit for carrier insertion into the inner membrane. These findings provide insights into the human carrier translocation pathway at molecular resolution and establish the TOM-TIM22 supercomplex as a central organizing unit of mitochondrial carrier import.
History
DepositionSep 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial import receptor subunit TOM5 homolog
B: Mitochondrial import receptor subunit TOM5 homolog
C: Mitochondrial import receptor subunit TOM6 homolog
D: Mitochondrial import receptor subunit TOM6 homolog
E: Mitochondrial import receptor subunit TOM7 homolog
F: Mitochondrial import receptor subunit TOM7 homolog
G: Mitochondrial import receptor subunit TOM22 homolog
H: Mitochondrial import receptor subunit TOM22 homolog
I: Mitochondrial import receptor subunit TOM40 homolog
J: Mitochondrial import receptor subunit TOM40 homolog
K: Mitochondrial GTP/GDP carrier protein 1
L: Mitochondrial GTP/GDP carrier protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,46745
Polymers214,02912
Non-polymers20,43833
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Mitochondrial import receptor subunit ... , 5 types, 10 molecules ABCDEFGHIJ

#1: 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: HEK293F / References: UniProt: Q8N4H5
#2: 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: HEK293F / References: UniProt: Q96B49
#3: 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: HEK293F / References: UniProt: Q9P0U1
#4: 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: HEK293F / References: UniProt: Q9NS69
#5: 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: HEK293F / References: UniProt: O96008

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Protein , 1 types, 2 molecules KL

#6: Protein Mitochondrial GTP/GDP carrier protein 1


Mass: 33245.387 Da / Num. of mol.: 2 / Mutation: C222S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: W303-1a / Gene: GGC1, SHM1, YHM1, YDL198C, D1214 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P38988

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Non-polymers , 2 types, 33 molecules

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


Mass: 790.145 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#8: Chemical
ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C16H34

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Details

Has ligand of interestN
Has protein modificationN

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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: Human TOM complex with substrate Tim22-GGC1-sfGFP / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293F / Cellular location: mitochondria / Organelle: mitochondria
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293F
Buffer solutionpH: 7.4
Details: 20 mM HEPES-NaOH pH 7.4, 100 mM NaCl, 0.06% digitonin
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMsodium chlorideNaCl1
30.6 mg/mLdigitonin1
SpecimenConc.: 3.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K
Details: 1.5 s blot time, 5 s wait time, 100% humidity, and 6 degree centigrade

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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: 130000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.44 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 15770
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.6particle selectionTemplate Picker
2EPU3 5 1.6034image acquisition
4cryoSPARC4.6CTF correctionPatch CTF Estimation
9PHENIX1.20.1-4487model refinement
10cryoSPARC4.6initial Euler assignmentAb-Initio Reconstruction
13cryoSPARC4.63D reconstructionNon-uniform Refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2551124
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 614218 / Symmetry type: POINT
Atomic model buildingDetails: The initial model was generated by ModelAngelo / Source name: Other / Type: in silico model

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