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- PDB-8i0k: Cryo-electron microscopic structure of the 2-oxoglutarate dehydro... -

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Basic information

Entry
Database: PDB / ID: 8i0k
TitleCryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase(E1) with TCAIM complex
Components
  • 2-oxoglutarate dehydrogenase complex component E1
  • T-cell activation inhibitor, mitochondrial
KeywordsPROTEIN BINDING / OGDH / proteostasis / DNAJC
Function / homology
Function and homology information


: / olfactory bulb mitral cell layer development / OGDH complex synthesizes succinyl-CoA from 2-OG / Glycine degradation / oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / succinyl-CoA metabolic process / tangential migration from the subventricular zone to the olfactory bulb / cerebellar cortex development / oxoglutarate dehydrogenase complex ...: / olfactory bulb mitral cell layer development / OGDH complex synthesizes succinyl-CoA from 2-OG / Glycine degradation / oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / succinyl-CoA metabolic process / tangential migration from the subventricular zone to the olfactory bulb / cerebellar cortex development / oxoglutarate dehydrogenase complex / striatum development / 2-oxoglutarate metabolic process / pyramidal neuron development / thalamus development / : / thiamine pyrophosphate binding / tricarboxylic acid cycle / heat shock protein binding / Mitochondrial protein degradation / glycolytic process / generation of precursor metabolites and energy / hippocampus development / mitochondrial membrane / protein-folding chaperone binding / mitochondrial matrix / mitochondrion / metal ion binding / nucleus
Similarity search - Function
Domain of unknown function DUF4461 / Domain of unknown function (DUF4461) / T-cell activation inhibitor, mitochondrial / Domain of unknown function DUF4460 / Domain of unknown function (DUF4460) / 2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal ...Domain of unknown function DUF4461 / Domain of unknown function (DUF4461) / T-cell activation inhibitor, mitochondrial / Domain of unknown function DUF4460 / Domain of unknown function (DUF4460) / 2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
Chem-8EL / THIAMINE DIPHOSPHATE / 2-oxoglutarate dehydrogenase complex component E1 / T-cell activation inhibitor, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsYu, X. / Yang, W. / Zhong, Y.H. / Ma, X.M. / Gao, Y.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) with TCAIM complex
Authors: Yu, X. / Yang, W. / Zhong, Y.H. / Ma, X.M. / Gao, Y.Z.
History
DepositionJan 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details
Item: _em_software.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-oxoglutarate dehydrogenase complex component E1
B: 2-oxoglutarate dehydrogenase complex component E1
C: T-cell activation inhibitor, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,9618
Polymers243,0213
Non-polymers9405
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15100 Å2
ΔGint-66 kcal/mol
Surface area77230 Å2

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein 2-oxoglutarate dehydrogenase complex component E1 / E1o / OGDC-E1 / OGDH-E1 / 2-oxoglutarate dehydrogenase / mitochondrial / Alpha-ketoglutarate ...E1o / OGDC-E1 / OGDH-E1 / 2-oxoglutarate dehydrogenase / mitochondrial / Alpha-ketoglutarate dehydrogenase / Alpha-KGDH-E1 / Thiamine diphosphate (ThDP)-dependent 2-oxoglutarate dehydrogenase


Mass: 103809.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGDH / Production host: Escherichia coli (E. coli)
References: UniProt: Q02218, oxoglutarate dehydrogenase (succinyl-transferring)
#2: Protein T-cell activation inhibitor, mitochondrial / Tolerance associated gene-1 protein / TOAG-1


Mass: 35402.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCAIM, C3orf23, TOAG1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N3R3

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Non-polymers , 4 types, 5 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-8EL / 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate


Mass: 426.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O7P2S
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 2-oxoglutarate dehydrogenase,OGDH and T cell activation inhibitor mitochondrial, TCAIM
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1342786 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00716949
ELECTRON MICROSCOPYf_angle_d0.85122963
ELECTRON MICROSCOPYf_dihedral_angle_d10.2172253
ELECTRON MICROSCOPYf_chiral_restr0.0922504
ELECTRON MICROSCOPYf_plane_restr0.0062983

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