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- EMDB-37965: E2 core of 2-oxoglutarate dehydrogenase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37965
TitleE2 core of 2-oxoglutarate dehydrogenase complex
Map data
Sample
  • Complex: mitochondrial enzyme complex
    • Protein or peptide: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial
KeywordsStructure of mitochondrial enzyme complex / TRANSFERASE
Function / homology
Function and homology information


L-lysine catabolic process to acetyl-CoA via saccharopine / succinyl-CoA metabolic process / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / 2-oxoglutarate metabolic process / tricarboxylic acid cycle / mitochondrial matrix / mitochondrion / nucleus
Similarity search - Function
: / Dihydrolipoamide succinyltransferase / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang SS / Zhang YT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21532004, 31570733 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
DepositionNov 3, 2023-
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_37965.png

Downloads & links

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Map

FileDownload / File: emd_37965.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 300 pix.
= 327. Å		1.09 Å/pix.
x 300 pix.
= 327. Å		1.09 Å/pix.
x 300 pix.
= 327. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0392
Minimum - Maximum-0.09135431 - 0.18103656
Average (Standard dev.)0.0008200308 (±0.008042545)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 327.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37965_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37965_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : mitochondrial enzyme complex

EntireName: mitochondrial enzyme complex
Components
  • Complex: mitochondrial enzyme complex
    • Protein or peptide: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial

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Supramolecule #1: mitochondrial enzyme complex

SupramoleculeName: mitochondrial enzyme complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Dihydrolipoyllysine-residue succinyltransferase component of 2-ox...

MacromoleculeName: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 49.038484 KDa
SequenceString: MLSRSRCVSR AFSRSLSAFQ KGNCPLGRRS LPGISLCQGP GYPDSRKIVI SNSSVLNVRF FRTTAVCKDD VITVKTPAFA ESVTEGDVR WEKAVGDTVA EDEVVCEIET DKTSVQVPSP ANGVIEALLV PDGGKVEGGT PLFTLRKTGA APAKAKPAEA P AAAAPKAE ...String:
MLSRSRCVSR AFSRSLSAFQ KGNCPLGRRS LPGISLCQGP GYPDSRKIVI SNSSVLNVRF FRTTAVCKDD VITVKTPAFA ESVTEGDVR WEKAVGDTVA EDEVVCEIET DKTSVQVPSP ANGVIEALLV PDGGKVEGGT PLFTLRKTGA APAKAKPAEA P AAAAPKAE PAVSAVPPPP AASIPTQMPP VPSPPQPLTS KPVSAVKPTA APPVAEPGAV KGLRAEHREK MNRMRQRIAQ RL KEAQNTC AMLTTFNEID MSNIQDMRAR HKEAFLKKHN LKLGFMSAFV KASAFALQEQ PVVNAVIDDT TKEVVYRDYI DIS VAVATP RGLVVPVIRN VETMNYADIE RTISELGEKA RKNELAIEDM DGGTFTISNG GVFGSLFGTP IINPPQSAIL GMHA IVDRP VAVGGKVEIR PMMYVALTYD HRLIDGREAV TFLRKIKAAV EDPRVLLLDL

UniProtKB: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 183521
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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