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- EMDB-73339: Cryo-EM structure of human Tom70 -

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Basic information

Entry
Database: EMDB / ID: EMD-73339
TitleCryo-EM structure of human Tom70
Map dataFinal map
Sample
  • Organelle or cellular component: Cryo-EM structure of human Tom70
    • Protein or peptide: Mitochondrial import receptor subunit TOM70
KeywordsMitochondrion outer membrane / Innate Immunity / Mitochondrial biogenesis / SARS-CoV-2 / TRANSLOCASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsSherer N / Yadav GP / Cho JH
Funding support United States, 2 items
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 GP / Cho JH
History
DepositionOct 15, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73339.png

Downloads & links

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Map

FileDownload / File: emd_73339.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0106
Minimum - Maximum-0.0017991058 - 1.8349459
Average (Standard dev.)0.00049597834 (±0.016365254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: raw map, unsharpened and unmasked

Fileemd_73339_additional_1.map
Annotationraw map, unsharpened and unmasked
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_73339_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_73339_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of human Tom70

EntireName: Cryo-EM structure of human Tom70
Components
  • Organelle or cellular component: Cryo-EM structure of human Tom70
    • Protein or peptide: Mitochondrial import receptor subunit TOM70

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Supramolecule #1: Cryo-EM structure of human Tom70

SupramoleculeName: Cryo-EM structure of human Tom70 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mitochondrial import receptor subunit TOM70

MacromoleculeName: Mitochondrial import receptor subunit TOM70 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.545742 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAASKPVEAA VVAAAVPSSG SGVGGGGTAG PGTGGLPRWQ LALAVGAPLL LGAGAIYLWS RQQRRREARG RGDASGLKRN SERKTPEGR ASPAPGSGHP EGPGAHLDMN SLDRAQAAKN KGNKYFKAGK YEQAIQCYTE AISLCPTEKN VDLSTFYQNR A AAFEQLQK ...String:
MAASKPVEAA VVAAAVPSSG SGVGGGGTAG PGTGGLPRWQ LALAVGAPLL LGAGAIYLWS RQQRRREARG RGDASGLKRN SERKTPEGR ASPAPGSGHP EGPGAHLDMN SLDRAQAAKN KGNKYFKAGK YEQAIQCYTE AISLCPTEKN VDLSTFYQNR A AAFEQLQK WKEVAQDCTK AVELNPKYVK ALFRRAKAHE KLDNKKECLE DVTAVCILEG FQNQQSMLLA DKVLKLLGKE KA KEKYKNR EPLMPSPQFI KSYFSSFTDD IISQPMLKGE KSDEDKDKEG EALEVKENSG YLKAKQYMEE ENYDKIISEC SKE IDAEGK YMAEALLLRA TFYLLIGNAN AAKPDLDKVI SLKEANVKLR ANALIKRGSM YMQQQQPLLS TQDFNMAADI DPQN ADVYH HRGQLKILLD QVEEAVADFD ECIRLRPESA LAQAQKCFAL YRQAYTGNNS SQIQAAMKGF EEVIKKFPRC AEGYA LYAQ ALTDQQQFGK ADEMYDKCID LEPDNATTYV HKGLLQLQWK QDLDRGLELI SKAIEIDNKC DFAYETMGTI EVQRGN MEK AIDMFNKAIN LAKSEMEMAH LYSLCDAAHA QTEVAKKYGL KPPTL

UniProtKB: Mitochondrial import receptor subunit TOM70

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7
Details: 20 mM HEPES (pH 7), 80 mM NaCl, 3 mM TCEP, 0.05% CHAPS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 0.05% Chaps added immediately before vitrification.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Average exposure time: 2.6 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2627413
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio in cryoSPARC v3.3.1
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC (ver. 3.3.1), DeepEMhancer) / Number images used: 372624
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

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

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