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- EMDB-31889: Tom20 subunits -

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Basic information

Entry
Database: EMDB / ID: EMD-31889
TitleTom20 subunits
Map data
Sample
  • Complex: The translocase of the outer mitochondrial membrane of Tom20 subunit
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog
KeywordsTom20 / Cryo-EM / TRANSLOCASE
Function / homology
Function and homology information


tRNA import into mitochondrion / TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / migrasome / mitochondria-associated endoplasmic reticulum membrane contact site / protein import into mitochondrial matrix / protein-transporting ATPase activity / Mitochondrial protein import / protein targeting to mitochondrion ...tRNA import into mitochondrion / TOM complex / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / migrasome / mitochondria-associated endoplasmic reticulum membrane contact site / protein import into mitochondrial matrix / protein-transporting ATPase activity / Mitochondrial protein import / protein targeting to mitochondrion / protein insertion into mitochondrial outer membrane / sperm midpiece / PINK1-PRKN Mediated Mitophagy / cell periphery / unfolded protein binding / mitochondrial outer membrane / Ub-specific processing proteases / mitochondrion
Similarity search - Function
Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor
Similarity search - Domain/homology
Mitochondrial import receptor subunit TOM20 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsLiu DS / Sui SF
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural basis of Tom20 and Tom22 cytosolic domains as the human TOM complex receptors.
Authors: Jiayue Su / Desheng Liu / Fan Yang / Mei-Qing Zuo / Chang Li / Meng-Qiu Dong / Shan Sun / Sen-Fang Sui /
Abstract: Mitochondrial preproteins synthesized in cytosol are imported into mitochondria by a multisubunit translocase of the outer membrane (TOM) complex. Functioned as the receptor, the TOM complex ...Mitochondrial preproteins synthesized in cytosol are imported into mitochondria by a multisubunit translocase of the outer membrane (TOM) complex. Functioned as the receptor, the TOM complex components, Tom 20, Tom22, and Tom70, recognize the presequence and further guide the protein translocation. Their deficiency has been linked with neurodegenerative diseases and cardiac pathology. Although several structures of the TOM complex have been reported by cryoelectron microscopy (cryo-EM), how Tom22 and Tom20 function as TOM receptors remains elusive. Here we determined the structure of TOM core complex at 2.53 Å and captured the structure of the TOM complex containing Tom22 and Tom20 cytosolic domains at 3.74 Å. Structural analysis indicates that Tom20 and Tom22 share a similar three-helix bundle structural feature in the cytosolic domain. Further structure-guided biochemical analysis reveals that the Tom22 cytosolic domain is responsible for binding to the presequence, and the helix H1 is critical for this binding. Altogether, our results provide insights into the functional mechanism of the TOM complex recognizing and transferring preproteins across the mitochondrial membrane.
History
DepositionSep 2, 2021-
Header (metadata) releaseSep 7, 2022-
Map releaseSep 7, 2022-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31889.png

Downloads & links

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Map

FileDownload / File: emd_31889.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 277.12 Å		1.08 Å/pix.
x 256 pix.
= 277.12 Å		1.08 Å/pix.
x 256 pix.
= 277.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0231
Minimum - Maximum-0.05933252 - 0.29469135
Average (Standard dev.)0.00006224322 (±0.0016656595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The translocase of the outer mitochondrial membrane of Tom20 subunit

EntireName: The translocase of the outer mitochondrial membrane of Tom20 subunit
Components
  • Complex: The translocase of the outer mitochondrial membrane of Tom20 subunit
    • Protein or peptide: Mitochondrial import receptor subunit TOM20 homolog

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Supramolecule #1: The translocase of the outer mitochondrial membrane of Tom20 subunit

SupramoleculeName: The translocase of the outer mitochondrial membrane of Tom20 subunit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Mitochondrial import receptor subunit TOM20 homolog

MacromoleculeName: Mitochondrial import receptor subunit TOM20 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.319862 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MVGRNSAIAA GVCGALFIGY CIYFDRKRRS DPNFKNRLRE RRKKQKLAKE RAGLSKLPDL KDAEAVQKFF LEEIQLGEEL LAQGEYEKG VDHLTNAIAV CGQPQQLLQV LQQTLPPPVF QMLLTKLPTI SQRIVSAQSL AEDDVE

UniProtKB: Mitochondrial import receptor subunit TOM20 homolog

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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: 7.4
Sugar embeddingMaterial: Digitonin
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 347600
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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