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- PDB-8b4i: Cryo-EM structure of the Neurospora crassa TOM core complex at 3.... -

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Basic information

Entry
Database: PDB / ID: 8b4i
TitleCryo-EM structure of the Neurospora crassa TOM core complex at 3.3 angstrom
Components
  • (Mitochondrial import receptor subunit ...) x 2
  • TOM6
  • TOM7
  • Translocase of outer mitochondrial membrane subunit 5
KeywordsMEMBRANE PROTEIN / Complex / outer membrane / mitochondria / TOM / translocase / neurospora crassa
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / protein targeting to mitochondrion / porin activity / pore complex / protein transmembrane transporter activity / mitochondrial outer membrane
Similarity search - Function
Mitochondrial import receptor subunit Tom22, fungi / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Tom40 / Eukaryotic porin/Tom40 ...Mitochondrial import receptor subunit Tom22, fungi / Mitochondrial import receptor subunit Tom40, fungi / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily
Similarity search - Domain/homology
Chem-DU0 / DIUNDECYL PHOSPHATIDYL CHOLINE / Mitochondrial import receptor subunit TOM40 / Mitochondrial import receptor subunit tom22 / Translocase of outer mitochondrial membrane subunit 5 / TOM7 / TOM6
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsOrnelas, P. / Kuehlbrandt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Two conformations of the Tom20 preprotein receptor in the TOM holo complex.
Authors: Pamela Ornelas / Thomas Bausewein / Janosch Martin / Nina Morgner / Stephan Nussberger / Werner Kühlbrandt /
Abstract: The TOM complex is the main entry point for precursor proteins (preproteins) into mitochondria. Preproteins containing targeting sequences are recognized by the TOM complex and imported into ...The TOM complex is the main entry point for precursor proteins (preproteins) into mitochondria. Preproteins containing targeting sequences are recognized by the TOM complex and imported into mitochondria. We have determined the structure of the TOM core complex from by single-particle electron cryomicroscopy at 3.3 Å resolution, showing its interaction with a bound preprotein at 4 Å resolution, and of the TOM holo complex including the Tom20 receptor at 6 to 7 Å resolution. TOM is a transmembrane complex consisting of two β-barrels, three receptor subunits, and three short transmembrane subunits. Tom20 has a transmembrane helix and a receptor domain on the cytoplasmic side. We propose that Tom20 acts as a dynamic gatekeeper, guiding preproteins into the pores of the TOM complex. We analyze the interactions of Tom20 with other TOM subunits, present insights into the structure of the TOM holo complex, and suggest a translocation mechanism.
History
DepositionSep 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial import receptor subunit Tom40
B: Mitochondrial import receptor subunit Tom40
C: Mitochondrial import receptor subunit Tom22
D: Mitochondrial import receptor subunit Tom22
E: Translocase of outer mitochondrial membrane subunit 5
F: Translocase of outer mitochondrial membrane subunit 5
G: TOM6
H: TOM6
I: TOM7
J: TOM7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,33019
Polymers147,57310
Non-polymers4,7579
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21880 Å2
ΔGint-200 kcal/mol
Surface area56450 Å2

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Components

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Mitochondrial import receptor subunit ... , 2 types, 4 molecules ABCD

#1: Protein Mitochondrial import receptor subunit Tom40


Mass: 38184.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: A0A0B0E409
#2: Protein Mitochondrial import receptor subunit Tom22


Mass: 17657.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Production host: Neurospora crassa (fungus) / References: UniProt: A0A0B0ECE8

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Translocase of outer mitochondrial membrane subunit 5 / Uncharacterized protein B1O14.260


Mass: 5405.200 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: F5HBE8

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Protein , 2 types, 4 molecules GHIJ

#4: Protein TOM6


Mass: 6470.329 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q9C1J1
#5: Protein TOM7 / Tom7-domain-containing protein


Mass: 6069.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus) / References: UniProt: Q9C1J0

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Non-polymers , 2 types, 9 molecules

#6: 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
#7: 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

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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

Component
IDNameTypeEntity IDParent-IDSource
1Translocase of the outer mitochondrial membrane core complex of Neurospora CrassaCOMPLEX#1-#50MULTIPLE SOURCES
2Mitochondrial import receptor subunit Tom22COMPLEX#21RECOMBINANT
3Translocase of the outer mitochondrial membrane core complex of Neurospora CrassaCOMPLEX#1, #3-#51NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrainOrganelle
23Neurospora crassa (fungus)5141GR-107Mitochondria
32Neurospora crassa (fungus)5141
Source (recombinant)Organism: Neurospora crassa (fungus)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 306000 / Symmetry type: POINT

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