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- EMDB-73359: Cryo-EM structure of human Tom70 in complex with Hsp90 C-terminal... -

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Basic information

Entry
Database: EMDB / ID: EMD-73359
TitleCryo-EM structure of human Tom70 in complex with Hsp90 C-terminal EEVD peptide
Map datafinal map
Sample
  • Organelle or cellular component: Cryo-EM structure of human Tom70 in complex with Hsp90 C-terminal EEVD peptide
    • Protein or peptide: Mitochondrial import receptor subunit TOM70
    • Protein or peptide: Heat shock protein HSP 90-alpha
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 / response to thyroxine / protein insertion into mitochondrial outer membrane / protein insertion into mitochondrial inner membrane / negative regulation of cell growth involved in cardiac muscle cell development / Mitochondrial protein import / : / : / sperm plasma membrane ...mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / response to thyroxine / protein insertion into mitochondrial outer membrane / protein insertion into mitochondrial inner membrane / negative regulation of cell growth involved in cardiac muscle cell development / Mitochondrial protein import / : / : / sperm plasma membrane / sperm mitochondrial sheath / sulfonylurea receptor binding / CTP binding / Scavenging by Class F Receptors / positive regulation of protein polymerization / vRNP Assembly / UTP binding / mitochondrial transport / dATP binding / telomerase holoenzyme complex assembly / chaperone-mediated autophagy / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / Uptake and function of diphtheria toxin / positive regulation of cell size / dendritic growth cone / protein import into mitochondrial matrix / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / response to salt stress / transmembrane protein transporter activity / protein folding chaperone complex / HSF1-dependent transactivation / response to unfolded protein / cardiac muscle cell apoptotic process / regulation of protein-containing complex assembly / Attenuation phase / HSF1 activation / enzyme-substrate adaptor activity / neurofibrillary tangle assembly / chaperone-mediated protein complex assembly / axonal growth cone / telomere maintenance via telomerase / positive regulation of lamellipodium assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / RHOBTB2 GTPase cycle / Dengue virus activates/modulates innate and adaptive immune responses / nitric oxide metabolic process / response to cold / protein unfolding / positive regulation of defense response to virus by host / skeletal muscle contraction / Signaling by ERBB2 / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of telomere maintenance via telomerase / endocytic vesicle lumen / DNA polymerase binding / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle contraction / Recruitment of mitotic centrosome proteins and complexes / lysosomal lumen / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / activation of innate immune response / ESR-mediated signaling / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein tyrosine kinase binding / AURKA Activation by TPX2 / Constitutive Signaling by Overexpressed ERBB2 / nitric-oxide synthase regulator activity / ATP-dependent protein folding chaperone / VEGFR2 mediated vascular permeability / PINK1-PRKN Mediated Mitophagy / brush border membrane / response to cocaine / cellular response to virus / positive regulation of protein import into nucleus / myelin sheath / neuron migration / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants
Similarity search - Function
Tetratricopeptide repeat / Tetratricopeptide repeat / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / TPR repeat region circular profile. ...Tetratricopeptide repeat / Tetratricopeptide repeat / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Mitochondrial import receptor subunit TOM70 / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 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: Cryo-EM structure of human Tom70 in complex with Hsp90 C-terminal EEVD peptide
Authors: Sherer N / Yadav GP / Cho JH
History
DepositionOct 16, 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_73359.png

Downloads & links

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Map

FileDownload / File: emd_73359.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 280 pix.
= 232.96 Å		0.83 Å/pix.
x 280 pix.
= 232.96 Å		0.83 Å/pix.
x 280 pix.
= 232.96 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0281
Minimum - Maximum-0.0017706171 - 1.9485629
Average (Standard dev.)0.000827769 (±0.02159895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 232.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Raw map before sharpening

Fileemd_73359_additional_1.map
AnnotationRaw map before sharpening
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map b

Fileemd_73359_half_map_1.map
Annotationhalf map b
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map a

Fileemd_73359_half_map_2.map
Annotationhalf map a
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 in complex with Hsp90 C-terminal...

EntireName: Cryo-EM structure of human Tom70 in complex with Hsp90 C-terminal EEVD peptide
Components
  • Organelle or cellular component: Cryo-EM structure of human Tom70 in complex with Hsp90 C-terminal EEVD peptide
    • Protein or peptide: Mitochondrial import receptor subunit TOM70
    • Protein or peptide: Heat shock protein HSP 90-alpha

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Supramolecule #1: Cryo-EM structure of human Tom70 in complex with Hsp90 C-terminal...

SupramoleculeName: Cryo-EM structure of human Tom70 in complex with Hsp90 C-terminal EEVD peptide
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: 67.432586 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 KPPT

UniProtKB: Mitochondrial import receptor subunit TOM70

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Macromolecule #2: Heat shock protein HSP 90-alpha

MacromoleculeName: Heat shock protein HSP 90-alpha / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-chaperonin molecular chaperone ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.245294 KDa
SequenceString:
YDTSRMEEVD

UniProtKB: Heat shock protein HSP 90-alpha

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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

Concentration4 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
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 / Number real images: 5301 / 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: 2516289
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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC (ver. 3.3.1), DeepEMhancer) / Number images used: 353087
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-9yr4:
Cryo-EM structure of human Tom70 in complex with Hsp90 C-terminal EEVD peptide

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