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- EMDB-49490: Structure of native octahedral assembly of D. discoideum Odo2 -

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Basic information

Entry
Database: EMDB / ID: EMD-49490
TitleStructure of native octahedral assembly of D. discoideum Odo2
Map data
Sample
  • Complex: Octahedral assembly of D. discoideum Odo2
    • Protein or peptide: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial
KeywordsAcyltransferase / TRANSFERASE
Function / homology
Function and homology information


Glycine degradation / OGDH complex synthesizes succinyl-CoA from 2-OG / Protein lipoylation / OADH complex synthesizes glutaryl-CoA from 2-OA / L-lysine catabolic process to acetyl-CoA via L-saccharopine / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / tricarboxylic acid cycle / mitochondrion
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 speciesDictyostelium discoideum AX2 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.72 Å
AuthorsHoogerbrugge G / Keatinge-Clay AT / Marcotte EM
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM106112 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM122480 United States
Department of Defense (DOD, United States)W911NF-12-1-0390 United States
Welch FoundationF-1712 United States
Welch FoundationF-1515 United States
CitationJournal: Mol Cell Proteomics / Year: 2026
Title: Serendipity and the Slime Mold: A Visual Survey of High-Molecular-Weight Protein Assemblies Reveals the Structure of the Polyketide Synthase Pks16.
Authors: Gabriel Hoogerbrugge / Adrian T Keatinge-Clay / Edward M Marcotte /
Abstract: Large macromolecular assemblies are integral to most cellular processes, making their identification and structural characterization an important strategy for advancing our understanding of protein ...Large macromolecular assemblies are integral to most cellular processes, making their identification and structural characterization an important strategy for advancing our understanding of protein functions. In this pilot study, we investigated large multiprotein assemblies from the cytoplasm of the slime mold Dictyostelium discoideum using shotgun electron microscopy, the combined application of mass spectrometry-based proteomics and cryo-EM to heterogenous mixtures of proteins. With its similarities in cell structure and behavior to mammalian cells, D. discoideum has long served as an invaluable model organism, particularly in the study of immune cell chemotaxis, phagocytosis, bacterial infection, and other processes. We subjected D. discoideum soluble protein complexes to two-step fractionation, performing size-exclusion chromatography followed by mixed-bed ion-exchange chromatography. Isolated fractions containing a subset of high molecular weight-scale protein assemblies were subsequently analyzed using mass spectrometry to identify the proteins and cryo-EM to characterize their structures. Mass spectrometry analysis revealed 179 unique proteins in the isolated fractions, then single-particle cryo-EM analysis generated distinct 2D projections of several visually distinctive protein assemblies, from which we successfully identified and reconstructed three major protein complexes: the 20S proteasome, the dihydrolipoyllysine-residue succinyltransferase (Odo2) of the mitochondrial 2-oxoglutarate dehydrogenase complex, and polyketide synthase 16 (Pks16), thought to be the primary fatty acid synthase of D. discoideum. Based on the Pks16 structure, the first of the 40 D. discoideum PKSs to be experimentally determined, models for the full set of D. discoideum PKSs were constructed with help from AlphaFold 3. Comparative analysis enabled structural characterization of their reaction chambers. Shotgun EM thus provides a view of proteins in their native or near-native biological conformations and scaling up this approach offers an effective route to characterize new structures of multiprotein assemblies directly from complex samples.
History
DepositionFeb 27, 2025-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49490.png

Downloads & links

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Map

FileDownload / File: emd_49490.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.75 Å/pix.
x 256 pix.
= 447.846 Å		1.75 Å/pix.
x 256 pix.
= 447.846 Å		1.75 Å/pix.
x 256 pix.
= 447.846 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7494 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.147
Minimum - Maximum-0.20223145 - 0.48900616
Average (Standard dev.)0.00016622353 (±0.025589228)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 447.8464 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49490_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49490_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49490_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Octahedral assembly of D. discoideum Odo2

EntireName: Octahedral assembly of D. discoideum Odo2
Components
  • Complex: Octahedral assembly of D. discoideum Odo2
    • Protein or peptide: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial

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Supramolecule #1: Octahedral assembly of D. discoideum Odo2

SupramoleculeName: Octahedral assembly of D. discoideum Odo2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Dictyostelium discoideum AX2 (eukaryote)

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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 / EC number: dihydrolipoyllysine-residue succinyltransferase
Source (natural)Organism: Dictyostelium discoideum AX2 (eukaryote)
Molecular weightTheoretical: 47.689219 KDa
SequenceString: MRSATKLIKN VNINRCVQSN VVRSTSRLIN NNSINTVRQF TSSSSSSFTS LFNNNNVNNT NIKYQRFYSS ANDVVIKVPS MGDSISEGT IVAWTKNVGD SVRVDEVVCS IETDKVTIDI NAPVSGTIVE LFAKEGENVT VGNDLYKIAK GEVAAAPKVE A PKAAEAPK ...String:
MRSATKLIKN VNINRCVQSN VVRSTSRLIN NNSINTVRQF TSSSSSSFTS LFNNNNVNNT NIKYQRFYSS ANDVVIKVPS MGDSISEGT IVAWTKNVGD SVRVDEVVCS IETDKVTIDI NAPVSGTIVE LFAKEGENVT VGNDLYKIAK GEVAAAPKVE A PKAAEAPK AAAPTPAPKA AETPKAAPAP KSEAPTPAPK STTTTTSTGP SETRVKMTRI RQRTAQRLKD SQNTAAMLTT FN ELDMSAL MNMRKTYKDE FEKKHGVKFG FMSAFVKAST IALKEQPIVN ASVEENDIVY HNNVNINVAV SAPRGLVVPV IRN CENLSF ADIEKEIGRL SGLARNDALA IEDSIGGTFT ISNGGVFGSM FGTPIINPPQ SAILGMHAIK DRPYVVNGQV VVRP IMYLA LTYDHRIIDG REAVTFLKKI KDVLENPERI LLEL

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: 7.4
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 200 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 836
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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