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- EMDB-60277: TOM core complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60277
TitleTOM core complex
Map data
Sample
  • Complex: TOM complex with whole Tom20
Keywordsmitochondria / transport / membrane protein complex / PROTEIN TRANSPORT
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.62 Å
AuthorsTian XY / Su JY / Sui SF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92254306 China
CitationJournal: PNAS Nexus / Year: 2024
Title: Structure of the intact Tom20 receptor in the human translocase of the outer membrane complex.
Authors: Jiayue Su / Xuyang Tian / Ziyi Wang / Jiawen Yang / Shan Sun / Sen-Fang Sui /
Abstract: The translocase of the outer membrane (TOM) complex serves as the main gate for preproteins entering mitochondria and thus plays a pivotal role in sustaining mitochondrial stability. Precursor ...The translocase of the outer membrane (TOM) complex serves as the main gate for preproteins entering mitochondria and thus plays a pivotal role in sustaining mitochondrial stability. Precursor proteins, featuring amino-terminal targeting signals (presequences) or internal targeting signals, are recognized by the TOM complex receptors Tom20, Tom22, and Tom70, and then translocated into mitochondria through Tom40. By using chemical cross-linking to stabilize Tom20 in the TOM complex, this study unveils the structure of the human TOM holo complex, encompassing the intact Tom20 component, at a resolution of approximately 6 Å by cryo-electron microscopy. Our structure shows the TOM holo complex containing only one Tom20 subunit, which is located right at the center of the complex and stabilized by extensive interactions with Tom22, Tom40, and Tom6. Based on the structure, we proposed a possible translocation mode of TOM complex, by which different receptors could work simultaneously to ensure that the preproteins recognized by them are all efficiently translocated into the mitochondria.
History
DepositionMay 27, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60277.png

Downloads & links

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Map

FileDownload / File: emd_60277.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 303.1 Å		1.08 Å/pix.
x 280 pix.
= 303.1 Å		1.08 Å/pix.
x 280 pix.
= 303.1 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.344
Minimum - Maximum-0.7214765 - 1.8150451
Average (Standard dev.)0.004454317 (±0.033653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 303.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60277_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60277_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : TOM complex with whole Tom20

EntireName: TOM complex with whole Tom20
Components
  • Complex: TOM complex with whole Tom20

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Supramolecule #1: TOM complex with whole Tom20

SupramoleculeName: TOM complex with whole Tom20 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 168.3 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

BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC7H15NO4SMOPS
150.0 mMKClpotassium chloride
0.1 %C56H92O29DIG
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 282 K

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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 / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1151405
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7vdd

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99493
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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