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- EMDB-3761: Cryo-EM structure of the TOM core complex from Neurospora crassa -

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Basic information

Entry
Database: EMDB / ID: EMD-3761
TitleCryo-EM structure of the TOM core complex from Neurospora crassa
Map dataTOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7
Sample
  • Complex: TOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7
    • Protein or peptide: Mitochondrial import receptor subunit tom40
KeywordsTOM-Complex / Protein Import / Mitochondria / Cryo-EM / PROTEIN TRANSPORT
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
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) / Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsBausewein T / Mills DJ
Funding support Germany, 1 items
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, 2017-
Header (metadata) releaseAug 16, 2017-
Map releaseAug 16, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0568
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0568
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5o8o
  • Surface level: 0.0568
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5o8o
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3761.png

Downloads & links

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Map

FileDownload / File: emd_3761.map.gz / Format: CCP4 / Size: 23 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 182 pix.
= 203.84 Å		1.12 Å/pix.
x 182 pix.
= 203.84 Å		1.12 Å/pix.
x 182 pix.
= 203.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0568 / Movie #1: 0.0568
Minimum - Maximum-0.07076823 - 0.18937553
Average (Standard dev.)0.00285874 (±0.011047585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-90
Dimensions182182182
Spacing182182182
CellA=B=C: 203.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z182182182
origin x/y/z0.0000.0000.000
length x/y/z203.840203.840203.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-90-90-90
NC/NR/NS182182182
D min/max/mean-0.0710.1890.003

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Supplemental data

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Sample components

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Entire : TOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7

EntireName: TOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7
Components
  • Complex: TOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7
    • Protein or peptide: Mitochondrial import receptor subunit tom40

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Supramolecule #1: TOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7

SupramoleculeName: TOM core complex consisting of Tom40, Tom22, Tom5, Tom6 and Tom7
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Neurospora crassa (fungus) / Strain: GR-107

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Macromolecule #1: Mitochondrial import receptor subunit tom40

MacromoleculeName: Mitochondrial import receptor subunit tom40 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: 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
Molecular weightTheoretical: 38.184797 KDa
SequenceString: MASFSTESPL AMLRDNAIYS SLSDAFNAFQ ERRKQFGLSN PGTIETIARE VQRDTLLTNY MFSGLRADVT KAFSLAPLFQ VSHQFAMGE RLNPYAFAAL YGTNQIFAQG NLDNEGALST RFNYRWGDRT ITKTQFSIGG GQDMAQFEHE HLGDDFSASL K AINPSFLD ...String:
MASFSTESPL AMLRDNAIYS SLSDAFNAFQ ERRKQFGLSN PGTIETIARE VQRDTLLTNY MFSGLRADVT KAFSLAPLFQ VSHQFAMGE RLNPYAFAAL YGTNQIFAQG NLDNEGALST RFNYRWGDRT ITKTQFSIGG GQDMAQFEHE HLGDDFSASL K AINPSFLD GGLTGIFVGD YLQAVTPRLG LGLQAVWQRQ GLTQGPDTAI SYFARYKAGD WVASAQLQAQ GALNTSFWKK LT DRVQAGV DMTLSVAPSQ SMMGGLTKEG ITTFGAKYDF RMSTFRAQID SKGKLSCLLE KRLGAAPVTL TFAADVDHVT QQA KLGMSV SIEASDVDLQ EQQEGAQSLN IPF

UniProtKB: Mitochondrial import receptor subunit tom40

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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

Concentration1 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92144
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-5o8o:
N. crassa Tom40 model based on cryo-EM structure of the TOM core complex at 6.8 A

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