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- EMDB-15856: Cryo-EM structure of the Neurospora crassa TOM core complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-15856
TitleCryo-EM structure of the Neurospora crassa TOM core complex with Tom20 over both pores
Map data
Sample
  • Complex: Translocase of the outer mitochondrial membrane core complex of Neurospora Crassa
KeywordsComplex / outer membrane / mitochondria / membrane protein / TOM / translocase / neurospora crassa / TOM holo / Tom20
Biological speciesNeurospora crassa (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsOrnelas P / Kuehlbrandt W
Funding support Germany, 1 items
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 21, 2022-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15856.png

Downloads & links

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Map

FileDownload / File: emd_15856.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 260 pix.
= 321.36 Å		1.24 Å/pix.
x 260 pix.
= 321.36 Å		1.24 Å/pix.
x 260 pix.
= 321.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.236 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0064
Minimum - Maximum-0.013920841 - 0.023833169
Average (Standard dev.)0.0000719732 (±0.0011429576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 321.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15856_half_map_1.map
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AxesZYX

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Half map: #2

Fileemd_15856_half_map_2.map
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Sample components

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Entire : Translocase of the outer mitochondrial membrane core complex of N...

EntireName: Translocase of the outer mitochondrial membrane core complex of Neurospora Crassa
Components
  • Complex: Translocase of the outer mitochondrial membrane core complex of Neurospora Crassa

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Supramolecule #1: Translocase of the outer mitochondrial membrane core complex of N...

SupramoleculeName: Translocase of the outer mitochondrial membrane core complex of Neurospora Crassa
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Neurospora crassa (fungus) / Strain: GR-107 / Organelle: Mitochondria

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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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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