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- EMDB-61087: in situ E1 of 2-oxoglutarate dehydrogenase complex subtomogram av... -

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Basic information

Entry
Database: EMDB / ID: EMD-61087
Titlein situ E1 of 2-oxoglutarate dehydrogenase complex subtomogram averaging map
Map data
Sample
  • Organelle or cellular component: in situ E1-OGDC
Keywordsin situ E1-OGDC / STRUCTURAL PROTEIN
Biological speciesSus scrofa (pig)
Methodelectron tomography / cryo EM
AuthorsZhang SS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030056 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
DepositionAug 6, 2024-
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_61087.png

Downloads & links

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Map

FileDownload / File: emd_61087.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.)
3 Å/pix.
x 72 pix.
= 216. Å		3 Å/pix.
x 72 pix.
= 216. Å		3 Å/pix.
x 72 pix.
= 216. Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.06365549 - 0.13860148
Average (Standard dev.)0.00028039064 (±0.008740357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 216.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : in situ E1-OGDC

EntireName: in situ E1-OGDC
Components
  • Organelle or cellular component: in situ E1-OGDC

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Supramolecule #1: in situ E1-OGDC

SupramoleculeName: in situ E1-OGDC / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Sus scrofa (pig)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 41

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