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- EMDB-38163: Inner core of mammalian pyruvate dehydrogenase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-38163
TitleInner core of mammalian pyruvate dehydrogenase complex
Map data
Sample
  • Complex: Native pyruvate dehydrogenase complex
KeywordsComplex component / TRANSFERASE
Biological speciesSus scrofa (pig)
Methodsubtomogram averaging / cryo EM / Resolution: 12.0 Å
AuthorsSong Y / Chen M / Yang M / Li S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Protein Cell / Year: 2025
Title: Molecular architecture of mammalian pyruvate dehydrogenase complex.
Authors: Maofei Chen / Yutong Song / Sensen Zhang / Yitang Zhang / Xudong Chen / Minghui Zhang / Meng Han / Xin Gao / Sai Li / Maojun Yang /
History
DepositionNov 29, 2023-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38163.png

Downloads & links

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Map

FileDownload / File: emd_38163.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.66 Å/pix.
x 128 pix.
= 340.48 Å		2.66 Å/pix.
x 128 pix.
= 340.48 Å		2.66 Å/pix.
x 128 pix.
= 340.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.3
Minimum - Maximum-6.8329916 - 6.625976
Average (Standard dev.)-0.020471986 (±0.81976956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 340.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38163_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38163_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_38163_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 : Native pyruvate dehydrogenase complex

EntireName: Native pyruvate dehydrogenase complex
Components
  • Complex: Native pyruvate dehydrogenase complex

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Supramolecule #1: Native pyruvate dehydrogenase complex

SupramoleculeName: Native pyruvate dehydrogenase complex / type: complex / ID: 1 / Parent: 0
Details: Inner core of porcine pyruvate dehydrogenase complex
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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 3.2 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 reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 494
ExtractionNumber tomograms: 94 / Number images used: 499
Final angle assignmentType: OTHER / Software - Name: Dynamo

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