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- PDB-9yql: Cryo-EM structure of human Tom70 -

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Basic information

Entry
Database: PDB / ID: 9yql
TitleCryo-EM structure of human Tom70
ComponentsMitochondrial import receptor subunit TOM70
KeywordsTRANSLOCASE / Mitochondrion outer membrane / Innate Immunity / Mitochondrial biogenesis / SARS-CoV-2
Function / homology
Function and homology information


mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein insertion into mitochondrial inner membrane / negative regulation of cell growth involved in cardiac muscle cell development / response to thyroxine / Mitochondrial protein import / : / : / protein import into mitochondrial matrix ...mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein insertion into mitochondrial inner membrane / negative regulation of cell growth involved in cardiac muscle cell development / response to thyroxine / Mitochondrial protein import / : / : / protein import into mitochondrial matrix / transmembrane protein transporter activity / positive regulation of defense response to virus by host / activation of innate immune response / positive regulation of interferon-beta production / PINK1-PRKN Mediated Mitophagy / cellular response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / mitochondrial membrane / SARS-CoV-1 activates/modulates innate immune responses / regulation of apoptotic process / protein-macromolecule adaptor activity / mitochondrial outer membrane / Ub-specific processing proteases / SARS-CoV-2 activates/modulates innate and adaptive immune responses / mitochondrion / extracellular exosome / membrane
Similarity search - Function
Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Mitochondrial import receptor subunit TOM70
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsSherer, N. / Yadav, G.P. / Cho, J.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM152007 United States
Welch FoundationA-2028-20230405 United States
CitationJournal: To Be Published
Title: CryoEM structure of human Tom70
Authors: Sherer, N. / Yadav, G.P. / Cho, J.H.
History
DepositionOct 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 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 TOM70


Theoretical massNumber of molelcules
Total (without water)67,5461
Polymers67,5461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Mitochondrial import receptor subunit TOM70 / Mitochondrial precursor proteins import receptor / Translocase of outer membrane 70 kDa subunit / ...Mitochondrial precursor proteins import receptor / Translocase of outer membrane 70 kDa subunit / Translocase of outer mitochondrial membrane protein 70


Mass: 67545.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOMM70, KIAA0719, TOM70, TOMM70A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94826
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: Cryo-EM structure of human Tom70 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7
Details: 20 mM HEPES (pH 7), 80 mM NaCl, 3 mM TCEP, 0.05% CHAPS
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 0.05% Chaps added immediately before vitrification

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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: 2400 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.6 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.1particle selection
2EPU3.12image acquisition
4cryoSPARC3.3.1CTF correction
9cryoSPARC3.3.1initial Euler assignment
10cryoSPARC3.3.1final Euler assignment
11cryoSPARC3.3.1classification
12cryoSPARC3.3.13D reconstruction
13DeepEMhancer3D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2627413
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 372624 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.57 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033855
ELECTRON MICROSCOPYf_angle_d0.6565180
ELECTRON MICROSCOPYf_dihedral_angle_d4.143512
ELECTRON MICROSCOPYf_chiral_restr0.037559
ELECTRON MICROSCOPYf_plane_restr0.005678

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