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- EMDB-30422: cryo-EM structure of the dimer of trimeric TOM complex -

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Basic information

Entry
Database: EMDB / ID: EMD-30422
Titlecryo-EM structure of the dimer of trimeric TOM complex
Map data
Sample
  • Complex: TOM translocase
Function / homology
Function and homology information


TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of type 2 mitophagy / Mitochondrial protein import / positive regulation of protein targeting to mitochondrion / protein targeting to mitochondrion / porin activity ...TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / protein insertion into mitochondrial outer membrane / mitochondria-associated endoplasmic reticulum membrane contact site / positive regulation of type 2 mitophagy / Mitochondrial protein import / positive regulation of protein targeting to mitochondrion / protein targeting to mitochondrion / porin activity / pore complex / protein import into mitochondrial matrix / protein transmembrane transporter activity / monoatomic ion transport / PINK1-PRKN Mediated Mitophagy / regulation of protein stability / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrion / membrane / cytosol
Similarity search - Function
Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / Mitochondrial import receptor subunit Tom22 / Mitochondrial import receptor subunit TOM7 / Mitochondrial import receptor subunit Tom22 / TOM7 family / Tom40 ...Mitochondrial import receptor subunit TOM5, metazoa / Mitochondrial import receptor subunit TOM6 homologue / Mitochondrial import receptor subunit TOM6 homolog / Mitochondrial outer membrane translocase complex, subunit Tom5 / Mitochondrial import receptor subunit or translocase / 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
Mitochondrial import receptor subunit TOM40 homolog / Mitochondrial import receptor subunit TOM5 homolog / Mitochondrial import receptor subunit TOM6 homolog / Mitochondrial import receptor subunit TOM22 homolog / Mitochondrial import receptor subunit TOM7 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsGuan Z / Yan L / Wang Q / Yan C / Yin P
CitationJournal: Cell Discov / Year: 2021
Title: Structural insights into assembly of human mitochondrial translocase TOM complex.
Authors: Zeyuan Guan / Ling Yan / Qiang Wang / Liangbo Qi / Sixing Hong / Zhou Gong / Chuangye Yan / Ping Yin /
History
DepositionAug 6, 2020-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateMay 19, 2021-
Current statusMay 19, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.43
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.43
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30422.png

Downloads & links

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Map

FileDownload / File: emd_30422.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 420 pix.
= 458.22 Å		1.09 Å/pix.
x 420 pix.
= 458.22 Å		1.09 Å/pix.
x 420 pix.
= 458.22 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.43
Minimum - Maximum-0.18370146 - 0.8179594
Average (Standard dev.)0.00044338155 (±0.038914356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 458.21997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z458.220458.220458.220
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.1840.8180.000

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Supplemental data

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Sample components

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Entire : TOM translocase

EntireName: TOM translocase
Components
  • Complex: TOM translocase

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Supramolecule #1: TOM translocase

SupramoleculeName: TOM translocase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293
Molecular weightTheoretical: 440 kDa/nm

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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

Concentration10 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 59704
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.0)

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