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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 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
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: To Be Published
Title: Cryo-EM structure of the Chaetomium thermophilum TOM core complex at 2.7 angstrom (pALDH treated)
Authors: Agip, A.N.A. / Ornelas, P. / Yang, T.J. / Ermanno, U. / Haeder, S. / McDowell, M.A. / Kuehlbrandt, W.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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