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- EMDB-38716: The conformation of E3 with PSBD in E2 components of pyruvate deh... -

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Entry
Database: EMDB / ID: EMD-38716
TitleThe conformation of E3 with PSBD in E2 components of pyruvate dehydrogenase complex
Map data
Sample
  • Complex: The conformation of E3 with PSBD in E2 components of pyruvate dehydrogenase complex
Keywordsdihydrolipoyl dehydrogenase / dihydrolipoyl transacetylase / peripheral subunit-binding domain / STRUCTURAL PROTEIN
Biological speciesSus scrofa (pig)
Methodsubtomogram averaging / cryo EM / Resolution: 15.0 Å
AuthorsWang C / Zhang X / Chang YJ
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFA0507700 China
National Natural Science Foundation of China (NSFC)32200980 China
CitationJournal: Nat Commun / Year: 2025
Title: Dynamics of the mammalian pyruvate dehydrogenase complex revealed by in-situ structural analysis.
Authors: Chen Wang / Cheng Ma / Yuanyou Xu / Shenghai Chang / Hangjun Wu / Chunlan Yan / Jinghua Chen / Yongping Wu / Shaoya An / Jiaqi Xu / Qin Han / Yujie Jiang / Zhinong Jiang / Xiakun Chu / ...Authors: Chen Wang / Cheng Ma / Yuanyou Xu / Shenghai Chang / Hangjun Wu / Chunlan Yan / Jinghua Chen / Yongping Wu / Shaoya An / Jiaqi Xu / Qin Han / Yujie Jiang / Zhinong Jiang / Xiakun Chu / Haichun Gao / Xing Zhang / Yunjie Chang /
Abstract: The multi-enzyme pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle and plays vital roles in metabolism, energy production, and cellular signaling. Although all ...The multi-enzyme pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle and plays vital roles in metabolism, energy production, and cellular signaling. Although all components have been individually characterized, the intact PDHc structure remains unclear, hampering our understanding of its composition and dynamical catalytic mechanisms. Here, we report the in-situ architecture of intact mammalian PDHc by cryo-electron tomography. The organization of peripheral E1 and E3 components varies substantially among the observed PDHcs, with an average of 21 E1 surrounding each PDHc core, and up to 12 E3 locating primarily along the pentagonal openings. In addition, we observed dynamic interactions of the substrate translocating lipoyl domains (LDs) with both E1 and E2, and the interaction interfaces were further analyzed by molecular dynamics simulations. By revealing intrinsic dynamics of PDHc peripheral compositions, our findings indicate a distinctive activity regulation mechanism, through which the number of E1, E3 and functional LDs may be coordinated to meet constantly changing demands of metabolism.
History
DepositionJan 15, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38716.png

Downloads & links

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Map

FileDownload / File: emd_38716.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
3.02 Å/pix.
x 80 pix.
= 241.6 Å		3.02 Å/pix.
x 80 pix.
= 241.6 Å		3.02 Å/pix.
x 80 pix.
= 241.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0397
Minimum - Maximum-0.17783229 - 0.4538747
Average (Standard dev.)-0.000030038933 (±0.01969462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 241.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38716_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #1

Fileemd_38716_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : The conformation of E3 with PSBD in E2 components of pyruvate deh...

EntireName: The conformation of E3 with PSBD in E2 components of pyruvate dehydrogenase complex
Components
  • Complex: The conformation of E3 with PSBD in E2 components of pyruvate dehydrogenase complex

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Supramolecule #1: The conformation of E3 with PSBD in E2 components of pyruvate deh...

SupramoleculeName: The conformation of E3 with PSBD in E2 components of pyruvate dehydrogenase complex
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 statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 6097
ExtractionNumber tomograms: 378 / Number images used: 120840
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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