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- EMDB-52652: CryoEM structure of the Chaetomium thermophilum TOM core complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-52652
TitleCryoEM structure of the Chaetomium thermophilum TOM core complex at 2.7 angstrom resolution (pALDH treated)
Map dataThe full map of the TOM core complex. pALDH treated sample.
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 import into mitochondrial matrix / protein insertion into mitochondrial outer membrane / 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: 2.7 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: To Be Published
Title: Cryo-EM structure of the Chaetomium thermophilum TOM core complex at 2.7 angstrom (pALDH treated)
Authors: Agip ANA / Ornelas P / Yang TJ / Ermanno U / Haeder S / McDowell MA / Kuehlbrandt W
History
DepositionJan 29, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52652.png

Downloads & links

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Map

FileDownload / File: emd_52652.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe full map of the TOM core complex. pALDH treated sample.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 560 pix.
= 320.88 Å		0.57 Å/pix.
x 560 pix.
= 320.88 Å		0.57 Å/pix.
x 560 pix.
= 320.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.573 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.91256684 - 1.212035
Average (Standard dev.)0.00035337306 (±0.020937707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 320.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52652_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The first half map of the TOM core complex. pALDH treated sample.

Fileemd_52652_half_map_1.map
AnnotationThe first half map of the TOM core complex. pALDH treated sample.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The second half map of the TOM core complex. pALDH treated sample.

Fileemd_52652_half_map_2.map
AnnotationThe second half map of the TOM core complex. pALDH treated sample.
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: Fusion with a FLAG tag at the c-terminus of the protein via a linker. Linker plus FLAG sequence: GSDYKDHDGDYKDDDDK,
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,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

Concentration1.9 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: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 34438 / Average exposure time: 3.0 sec. / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 215000
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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 345380
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

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
DetailsModelAngelo was used to build the initial model.
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9i6b:
CryoEM structure of the Chaetomium thermophilum TOM core complex at 2.7 angstrom resolution (pALDH treated)

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