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- EMDB-38335: Cryo-EM map of the E2 inner core component of pyruvate dehydrogen... -

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Basic information

Entry
Database: EMDB / ID: EMD-38335
TitleCryo-EM map of the E2 inner core component of pyruvate dehydrogenase complex
Map datad2
Sample
  • Complex: the E2 inner core pf pyruvate dehdrogeanse complex
KeywordsPDH / E2 / Dihydrolipoyl transacetylase / PROTEIN BINDING
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.79 Å
AuthorsKim H / Jeong MS / An MY / Jung HS
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C1009404 Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2024
Title: Comparative Analysis of Symmetry Parameters in the E2 Inner Core of the Pyruvate Dehydrogenase Complex.
Authors: Han-Ul Kim / Myeong Seon Jeong / Mi Young An / Yoon Ho Park / Sun Hee Park / Sang J Chung / Yoon-Sun Yi / Sangmi Jun / Young Kwan Kim / Hyun Suk Jung /
Abstract: Recent advances in cryo-electron microscopy (cryo-EM) have facilitated the high-resolution structural determination of macromolecular complexes in their native states, providing valuable insights ...Recent advances in cryo-electron microscopy (cryo-EM) have facilitated the high-resolution structural determination of macromolecular complexes in their native states, providing valuable insights into their dynamic behaviors. However, insufficient understanding or experience with the cryo-EM image processing parameters can result in the loss of biological meaning. In this paper, we investigate the dihydrolipoyl acetyltransferase (E2) inner core complex of the pyruvate dehydrogenase complex (PDC) and reconstruct the 3D maps using five different symmetry parameters. The results demonstrate that the reconstructions yield structurally identical 3D models even at a near-atomic structure. This finding underscores a crucial message for researchers engaging in single-particle analysis (SPA) with relatively user-friendly and convenient image processing software. This approach helps reduce the risk of missing critical biological details, such as the dynamic properties of macromolecules.
History
DepositionDec 16, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38335.png

Downloads & links

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Map

FileDownload / File: emd_38335.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationd2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 550 pix.
= 605. Å		1.1 Å/pix.
x 550 pix.
= 605. Å		1.1 Å/pix.
x 550 pix.
= 605. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.13157992 - 0.39361185
Average (Standard dev.)0.00079520245 (±0.016601171)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions550550550
Spacing550550550
CellA=B=C: 605.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: a

Fileemd_38335_half_map_1.map
Annotationa
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: b

Fileemd_38335_half_map_2.map
Annotationb
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : the E2 inner core pf pyruvate dehdrogeanse complex

EntireName: the E2 inner core pf pyruvate dehdrogeanse complex
Components
  • Complex: the E2 inner core pf pyruvate dehdrogeanse complex

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Supramolecule #1: the E2 inner core pf pyruvate dehdrogeanse complex

SupramoleculeName: the E2 inner core pf pyruvate dehdrogeanse complex / type: complex / ID: 1 / Parent: 0 / Details: Dihydrolipoyl transacetylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 700 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 26.0 µm / Nominal defocus min: 18.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69946
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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