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- PDB-5o8o: N. crassa Tom40 model based on cryo-EM structure of the TOM core ... -

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Basic information

Entry
Database: PDB / ID: 5o8o
TitleN. crassa Tom40 model based on cryo-EM structure of the TOM core complex at 6.8 A
ComponentsMitochondrial import receptor subunit tom40
KeywordsPROTEIN TRANSPORT / TOM-Complex / Protein Import / Mitochondria / Cryo-EM
Function / homology
Function and homology information


mitochondrial outer membrane translocase complex / protein import into mitochondrial matrix / porin activity / pore complex / protein transmembrane transporter activity
Similarity search - Function
Mitochondrial import receptor subunit Tom40, fungi / Tom40 / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin domain superfamily
Similarity search - Domain/homology
Mitochondrial import receptor subunit tom40
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsBausewein, T. / Mills, D.J. / Nussberger, S. / Nitschke, B. / Kuehlbrandt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Cell / Year: 2017
Title: Cryo-EM Structure of the TOM Core Complex from Neurospora crassa.
Authors: Thomas Bausewein / Deryck J Mills / Julian D Langer / Beate Nitschke / Stephan Nussberger / Werner Kühlbrandt /
Abstract: The TOM complex is the main entry gate for protein precursors from the cytosol into mitochondria. We have determined the structure of the TOM core complex by cryoelectron microscopy (cryo-EM). The ...The TOM complex is the main entry gate for protein precursors from the cytosol into mitochondria. We have determined the structure of the TOM core complex by cryoelectron microscopy (cryo-EM). The complex is a 148 kDa symmetrical dimer of ten membrane protein subunits that create a shallow funnel on the cytoplasmic membrane surface. In the core of the dimer, the β-barrels of the Tom40 pore form two identical preprotein conduits. Each Tom40 pore is surrounded by the transmembrane segments of the α-helical subunits Tom5, Tom6, and Tom7. Tom22, the central preprotein receptor, connects the two Tom40 pores at the dimer interface. Our structure offers detailed insights into the molecular architecture of the mitochondrial preprotein import machinery.
History
DepositionJun 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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

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Assembly

Deposited unit
A: Mitochondrial import receptor subunit tom40


Theoretical massNumber of molelcules
Total (without water)38,1851
Polymers38,1851
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19430 Å2
MethodPISA

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Components

#1: Protein Mitochondrial import receptor subunit tom40 / Protein MOM38 / Translocase of outer membrane 40 kDa subunit


Mass: 38184.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
References: UniProt: P24391

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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 core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Neurospora crassa (fungus) / Strain: GR-107
Buffer solutionpH: 7.2
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
13Folditmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92144 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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