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- PDB-9i6b: CryoEM structure of the Chaetomium thermophilum TOM core complex ... -

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Basic information

Entry
Database: PDB / ID: 9i6b
TitleCryoEM structure of the Chaetomium thermophilum TOM core complex at 2.7 angstrom resolution (pALDH treated)
Components
  • (Mitochondrial import receptor subunit ...) x 4
  • Import receptor subunit-like protein
KeywordsMEMBRANE PROTEIN / Mitochondria
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / porin activity / pore complex / protein import into mitochondrial matrix / protein transmembrane transporter activity / monoatomic ion transport / 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
Chem-DU0 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DIUNDECYL PHOSPHATIDYL CHOLINE / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsAgip, A.N.A. / Ornelas, P. / Yang, T.J. / Ermanno, U. / Haeder, S. / McDowell, M.A. / Kuehlbrandt, W.
Funding support Germany, 1items
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 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Mitochondrial import receptor subunit tom22
E: Mitochondrial import receptor subunit tom5
G: Mitochondrial import receptor subunit tom6
I: Import receptor subunit-like protein
A: Mitochondrial import receptor subunit (Tom40)-like protein
D: Mitochondrial import receptor subunit tom22
F: Mitochondrial import receptor subunit tom5
H: Mitochondrial import receptor subunit tom6
J: Import receptor subunit-like protein
B: Mitochondrial import receptor subunit (Tom40)-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,76129
Polymers159,10310
Non-polymers12,65819
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Mitochondrial import receptor subunit ... , 4 types, 8 molecules CDEFGHAB

#1: Protein Mitochondrial import receptor subunit tom22 / Mitochondrial import receptor subunit Tom22


Mass: 19237.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fusion with a FLAG tag at the c-terminus of the protein via a linker. Linker plus FLAG sequence: GSDYKDHDGDYKDDDDK,
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0026640
Production host: Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S6L5
#2: Protein/peptide Mitochondrial import receptor subunit tom5


Mass: 5345.150 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#3: Protein Mitochondrial import receptor subunit tom6 / Mitochondrial import receptor subunit Tom6


Mass: 9008.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Mitochondrial import receptor subunit Tom6
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S9G0
#5: Protein Mitochondrial import receptor subunit (Tom40)-like protein / Mitochondrial import receptor subunit Tom40


Mass: 37849.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Mitochondrial import receptor subunit Tom40
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S7S2

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Protein , 1 types, 2 molecules IJ

#4: Protein Import receptor subunit-like protein / Mitochondrial import receptor subunit tom7 / Tom7


Mass: 8110.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Mitochondrial import receptor subunit tom7,Tom7
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SE07

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Non-polymers , 3 types, 19 molecules

#6: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#7: Chemical
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


Mass: 516.752 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C32H52O5
#8: Chemical ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM

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Details

Has ligand of interestN
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: TOM / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightValue: 0.159 MDa / Experimental value: NO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMPotassium Phosphate BufferK2HPO4/KH2PO41
250 mMPotassium ChlorideKCl1
31 mMEthylenediaminetetraacetic acidEDTA1
41 mMTris (2-carboxyethyl) phosphineTCEP1
50.02 %Glyco-diosgeninGDN1
SpecimenConc.: 1.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: 215000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 70 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 34438
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameCategory
2EPUimage acquisition
4cryoSPARCCTF correction
7ISOLDEmodel fitting
8Cootmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 345380 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Details: ModelAngelo was used to build the initial model.
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model
RefinementHighest resolution: 2.7 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0078845
ELECTRON MICROSCOPYf_angle_d0.85512003
ELECTRON MICROSCOPYf_dihedral_angle_d17.693279
ELECTRON MICROSCOPYf_chiral_restr0.0541329
ELECTRON MICROSCOPYf_plane_restr0.0171434

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