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- EMDB-38711: The conformation of E1 with PSBD in E2 components of pyruvate deh... -

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Basic information

Entry
Database: EMDB / ID: EMD-38711
TitleThe conformation of E1 with PSBD in E2 components of pyruvate dehydrogenase complex
Map data
Sample
  • Complex: The conformation of E1 with PSBD in E2 components of pyruvate dehydrogenase complex
Keywordspyruvate dehydrogenase / dihydrolipoyl transacetylase / peripheral subunit-binding domain / STRUCTURAL PROTEIN
Biological speciesSus scrofa (pig)
Methodsubtomogram averaging / cryo EM / Resolution: 10.8 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: To Be Published
Title: Architecture and catalytic regulation mechanism of intact mammalian pyruvate dehydrogenase complex revealed by in-situ structural analysis
Authors: Wang C / Zhang X / Chang YJ
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_38711.png

Downloads & links

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Map

FileDownload / File: emd_38711.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.02 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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.081
Minimum - Maximum-0.21372063 - 0.6239433
Average (Standard dev.)0.00008714755 (±0.023445973)
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: #1

Fileemd_38711_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_38711_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 : The conformation of E1 with PSBD in E2 components of pyruvate deh...

EntireName: The conformation of E1 with PSBD in E2 components of pyruvate dehydrogenase complex
Components
  • Complex: The conformation of E1 with PSBD in E2 components of pyruvate dehydrogenase complex

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Supramolecule #1: The conformation of E1 with PSBD in E2 components of pyruvate deh...

SupramoleculeName: The conformation of E1 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: 10.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 6959
ExtractionNumber tomograms: 378 / Number images used: 44194
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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