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- EMDB-52658: CryoEM structure of the Chaetomium thermophilum TOM core complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-52658
TitleCryoEM structure of the Chaetomium thermophilum TOM core complex at 3.2 angstrom resolution
Map dataFull map generated by cryoSPARC.
Sample
  • Complex: TOM
    • Protein or peptide: Mitochondrial import receptor subunit tom22
    • Protein or peptide: Mitochondrial import receptor subunit Tom5
    • Protein or peptide: Mitochondrial import receptor subunit tom6
    • Protein or peptide: Import receptor subunit-like protein
    • Protein or peptide: Mitochondrial import receptor subunit (Tom40)-like protein
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
KeywordsMitochondria / MEMBRANE PROTEIN
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / protein import into mitochondrial matrix / protein transmembrane transporter activity / intracellular protein transport / mitochondrial outer membrane
Similarity search - Function
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
Mitochondrial import receptor subunit tom22 / Translocase of outer membrane 40 kDa subunit / Uncharacterized protein / Import receptor subunit-like protein
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsAgip ANA / Ornelas P / Yang TJ / Ermanno U / Haeder S / McDowell MA / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structures of TOM complexes with bound preproteins.
Authors: Ahmed-Noor A Agip / Pamela Ornelas / Tzu-Jing Yang / Ermanno Uboldi / Sabine Häder / Melanie A McDowell / Werner Kühlbrandt /
Abstract: Mitochondria import most of their proteins from the cytoplasm through the TOM complex. Preproteins containing targeting signals are recognized by the TOM receptor subunits and translocated by Tom40 ...Mitochondria import most of their proteins from the cytoplasm through the TOM complex. Preproteins containing targeting signals are recognized by the TOM receptor subunits and translocated by Tom40 across the outer mitochondrial membrane. We present four structures of the preprotein-bound and preprotein-free TOM core and holo complexes from the thermophilic fungus , obtained by single-particle electron cryomicroscopy. Our structures reveal the symmetric arrangement of two copies of the Tom20 receptor subunit in the TOM holo complex. Several different conformations of Tom20 within the TOM holo complex highlight the dynamic nature of the receptor. The structure of preprotein-bound Tom20 provides insight into the early stages of protein translocation.
History
DepositionJan 31, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52658.png

Downloads & links

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Map

FileDownload / File: emd_52658.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map generated by cryoSPARC.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 301.32 Å		0.84 Å/pix.
x 360 pix.
= 301.32 Å		0.84 Å/pix.
x 360 pix.
= 301.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.485
Minimum - Maximum-2.169185 - 3.6364763
Average (Standard dev.)0.0044517606 (±0.06754743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 301.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52658_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B generated by cryoSPARC.

Fileemd_52658_half_map_1.map
AnnotationHalf map B generated by cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A generated by cryoSPARC.

Fileemd_52658_half_map_2.map
AnnotationHalf map A generated by cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TOM

EntireName: TOM
Components
  • Complex: TOM
    • Protein or peptide: Mitochondrial import receptor subunit tom22
    • Protein or peptide: Mitochondrial import receptor subunit Tom5
    • Protein or peptide: Mitochondrial import receptor subunit tom6
    • Protein or peptide: Import receptor subunit-like protein
    • Protein or peptide: Mitochondrial import receptor subunit (Tom40)-like protein
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE

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Supramolecule #1: TOM

SupramoleculeName: TOM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 159 KDa

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Macromolecule #1: Mitochondrial import receptor subunit tom22

MacromoleculeName: Mitochondrial import receptor subunit tom22 / type: protein_or_peptide / ID: 1
Details: A linker followed by a FLAG tag were introduced at the c-terminus of Tom22, Mitochondrial import receptor subunit Tom22
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 19.237748 KDa
Recombinant expressionOrganism: Thermochaetoides thermophila DSM 1495 (fungus)
SequenceString:
MVQLVEVEDE HFTQPQPGPE EDDDEYTDTD SEISTESNFD PSEETLADRL HALRDMVPPA YRGWIYHKYE QTTSAVRKAL SFAGRAAWT VSVTALLVGV PFSLAYGEDQ QYAAMEQEQR MRELGGEVLT AGAPGSQGGG LTAEQVNAAL GRSEAKPALG S DYKDHDGD YKDDDDK

UniProtKB: Mitochondrial import receptor subunit tom22

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Macromolecule #2: Mitochondrial import receptor subunit Tom5

MacromoleculeName: Mitochondrial import receptor subunit Tom5 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 5.34515 KDa
SequenceString:
MFGGCQPPQP SPEELRAAEA EAASTIQRAI ATAAVLYLAP FIVDAVYKMF

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Macromolecule #3: Mitochondrial import receptor subunit tom6

MacromoleculeName: Mitochondrial import receptor subunit tom6 / type: protein_or_peptide / ID: 3 / Details: Mitochondrial import receptor subunit Tom6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 9.008387 KDa
SequenceString:
MPPKRVSYNS RRSLNPITGA YNALFVSENA SIVRSVVAFG LAVTFLASGW AEAILSCVPS PLVSSRQQQP PLTDLQKPCV NGLI

UniProtKB: Uncharacterized protein

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Macromolecule #4: Import receptor subunit-like protein

MacromoleculeName: Import receptor subunit-like protein / type: protein_or_peptide / ID: 4 / Details: Mitochondrial import receptor subunit Tom7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 8.110614 KDa
SequenceString:
MLALSEESKV RRGPSLRTIR LGADSKQERI SKLIEISRVV IHYGYLPMIL YLGYTRSEPK PSIIRLLSPL S

UniProtKB: Import receptor subunit-like protein

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Macromolecule #5: Mitochondrial import receptor subunit (Tom40)-like protein

MacromoleculeName: Mitochondrial import receptor subunit (Tom40)-like protein
type: protein_or_peptide / ID: 5 / Details: Mitochondrial import receptor subunit Tom40 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 37.849609 KDa
SequenceString: MASSTNSPLA FLRSNPVFAS LSDLYDAFQE RRQKLGLSNP GLVENIAKEV QRDVLTTNLM FSGLRADLTK AFSLNPLFQV SHQFAMGER LSPYTFAALY GTSKMFAQGN IDDQGNLSTT FNYRWTPSFT TKTRFQITPG ATGQDMAQFE HEYSGADFTA T IKALNPSF ...String:
MASSTNSPLA FLRSNPVFAS LSDLYDAFQE RRQKLGLSNP GLVENIAKEV QRDVLTTNLM FSGLRADLTK AFSLNPLFQV SHQFAMGER LSPYTFAALY GTSKMFAQGN IDDQGNLSTT FNYRWTPSFT TKTRFQITPG ATGQDMAQFE HEYSGADFTA T IKALNPSF LEGGLTGIFV GQYLQSITPK LSLGLEAVWQ RAGLTQGPDT AISYVGRYKT ENWIASAQLQ AQGALNASYW QR LGEKVQA GVDMTLSVNP GAAMMGGPTK EGITTFGAKY DFRMSTFRAQ IDTKGKLSCV LEKRVAAPVM MTFAADVDHF TQQ AKVGVG ISIEAGGEEL QDQQPAPNIP F

UniProtKB: Translocase of outer membrane 40 kDa subunit

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Macromolecule #6: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 10 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #7: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13...

MacromoleculeName: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
type: ligand / ID: 7 / Number of copies: 8 / Formula: DU0
Molecular weightTheoretical: 516.752 Da
Chemical component information

ChemComp-DU0:
2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol

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Macromolecule #8: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 8 / Number of copies: 1 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

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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

Concentration1.64 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMK2HPO4/KH2PO4Potassium Phosphate Buffer
50.0 mMKClPotassium Chloride
1.0 mMEDTAEthylenediaminetetraacetic acid
1.0 mMTCEPTris (2-carboxyethyl) phosphine
0.02 %GDNGlyco-diosgenin
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 15566 / Average exposure time: 3.3 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 326681
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9i7p:
CryoEM structure of the Chaetomium thermophilum TOM core complex at 3.2 angstrom resolution

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