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- EMDB-37968: E3 of 2-oxoglutarate dehydrogenase complex subtomogram averaging map -

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Basic information

Entry
Database: EMDB / ID: EMD-37968
TitleE3 of 2-oxoglutarate dehydrogenase complex subtomogram averaging map
Map data
Sample
  • Complex: mitochondrial complex E3 subunit
KeywordsStructure of mitochondrial enzyme complex / structural protein
Biological speciesSus scrofa (pig)
Methodsubtomogram averaging / cryo EM / Resolution: 12.2 Å
AuthorsZhang SS / Zhang YT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21532004, 31570733 China
CitationJournal: Nat Commun / Year: 2024
Title: Molecular architecture of the mammalian 2-oxoglutarate dehydrogenase complex.
Authors: Yitang Zhang / Maofei Chen / Xudong Chen / Minghui Zhang / Jian Yin / Zi Yang / Xin Gao / Sensen Zhang / Maojun Yang /
Abstract: The 2-oxoglutarate dehydrogenase complex (OGDHc) orchestrates a critical reaction regulating the TCA cycle. Although the structure of each OGDHc subunit has been solved, the architecture of the ...The 2-oxoglutarate dehydrogenase complex (OGDHc) orchestrates a critical reaction regulating the TCA cycle. Although the structure of each OGDHc subunit has been solved, the architecture of the intact complex and inter-subunit interactions still remain unknown. Here we report the assembly of native, intact OGDHc from Sus scrofa heart tissue using cryo-electron microscopy (cryo-EM), cryo-electron tomography (cryo-ET), and subtomogram averaging (STA) to discern native structures of the whole complex and each subunit. Our cryo-EM analyses revealed the E2o cubic core structure comprising eight homotrimers at 3.3-Å resolution. More importantly, the numbers, positions and orientations of each OGDHc subunit were determined by cryo-ET and the STA structures of the core were resolved at 7.9-Å with the peripheral subunits reaching nanometer resolution. Although the distribution of the peripheral subunits E1o and E3 vary among complexes, they demonstrate a certain regularity within the position and orientation. Moreover, we analyzed and validated the interactions between each subunit, and determined the flexible binding mode for E1o, E2o and E3, resulting in a proposed model of Sus scrofa OGDHc. Together, our results reveal distinctive factors driving the architecture of the intact, native OGDHc.
History
DepositionNov 3, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37968.png

Downloads & links

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Map

FileDownload / File: emd_37968.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 72 pix.
= 195.696 Å		2.72 Å/pix.
x 72 pix.
= 195.696 Å		2.72 Å/pix.
x 72 pix.
= 195.696 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0197
Minimum - Maximum-0.13895628 - 0.20392726
Average (Standard dev.)0.00026848854 (±0.011593414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 195.696 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37968_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37968_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mitochondrial complex E3 subunit

EntireName: mitochondrial complex E3 subunit
Components
  • Complex: mitochondrial complex E3 subunit

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Supramolecule #1: mitochondrial complex E3 subunit

SupramoleculeName: mitochondrial complex E3 subunit / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Sus scrofa (pig)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
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: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 8240
ExtractionNumber tomograms: 137 / Number images used: 17513
Final angle assignmentType: ANGULAR RECONSTITUTION

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