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- EMDB-35042: Cryo-EM structure of the the 2-oxoglutarate dehydrogenase (E1) wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-35042
TitleCryo-EM structure of the the 2-oxoglutarate dehydrogenase (E1) with TCAIM complex
Map data
Sample
  • Complex: 2-oxoglutarate dehydrogenase, OGDH and T cell activation inhibitor mitochondrial, TCAIM
    • Protein or peptide: 2-oxoglutarate dehydrogenase(E1)
    • Protein or peptide: T-cell activation inhibitor, mitochondrial
KeywordsTCAIM / Mitochondria / alpha ketoglutarate dehydrogenase / OGDH / proteostasis / DNAJC / single particle cryoEM / PROTEIN BINDING
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
2-oxoglutarate dehydrogenase complex component E1 / T-cell activation inhibitor, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsYu X / Yang W
Funding support China, 1 items
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 YH / Ma XM / Gao YZ
History
DepositionDec 26, 2022-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_35042.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.855 Å
Density
Contour LevelBy AUTHOR: 0.143
Minimum - Maximum-1.3874857 - 2.456897
Average (Standard dev.)-0.00267383 (±0.082382984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 218.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : 2-oxoglutarate dehydrogenase, OGDH and T cell activation inhibito...

EntireName: 2-oxoglutarate dehydrogenase, OGDH and T cell activation inhibitor mitochondrial, TCAIM
Components
  • Complex: 2-oxoglutarate dehydrogenase, OGDH and T cell activation inhibitor mitochondrial, TCAIM
    • Protein or peptide: 2-oxoglutarate dehydrogenase(E1)
    • Protein or peptide: T-cell activation inhibitor, mitochondrial

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Supramolecule #1: 2-oxoglutarate dehydrogenase, OGDH and T cell activation inhibito...

SupramoleculeName: 2-oxoglutarate dehydrogenase, OGDH and T cell activation inhibitor mitochondrial, TCAIM
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 2-oxoglutarate dehydrogenase(E1)

MacromoleculeName: 2-oxoglutarate dehydrogenase(E1) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
EC number: oxoglutarate dehydrogenase (succinyl-transferring)
Source (natural)Organism: Homo sapiens (human)
SequenceString: HNEMDEPMFT QPLMYKQIRK QKPVLQKYAE LLVSQGVVNQ PEYEEEISKY DKICEEAFAR SKDEKILHIK HWLDSPWPGF FTLDGQPRS MSCPSTGLTE DILTHIGNVA SSVPVENFTI HGGLSRILKT RGEMVKNRTV DWALAEYMAF GSLLKEGIHI R LSGQDVER ...String:
HNEMDEPMFT QPLMYKQIRK QKPVLQKYAE LLVSQGVVNQ PEYEEEISKY DKICEEAFAR SKDEKILHIK HWLDSPWPGF FTLDGQPRS MSCPSTGLTE DILTHIGNVA SSVPVENFTI HGGLSRILKT RGEMVKNRTV DWALAEYMAF GSLLKEGIHI R LSGQDVER GTFSHRHHVL HDQNVDKRTC IPMNHLWPNQ APYTVCNSSL SEYGVLGFEL GFAMASPNAL VLWEAQFGDF HN TAQCIID QFICPGQAKW VRQNGIVLLL PHGMEGMGPE HSSARPERFL QMCNDDPDVL PDLKEANFDI NQLYDCNWVV VNC STPGNF FHVLRRQILL PFRKPLIIFT PKSLLRHPEA RSSFDEMLPG THFQRVIPED GPAAQNPENV KRLLFCTGKV YYDL TRERK ARDMVGQVAI TRIEQLSPFP FDLLLKEVQK YPNAELAWCQ EEHKNQGYYD YVKPRLRTTI SRAKPVWYAG RDPAA APAT GNKKTHLTEL QRLLDTAFDL DVFKNFS

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Macromolecule #2: T-cell activation inhibitor, mitochondrial

MacromoleculeName: T-cell activation inhibitor, mitochondrial / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: TTLTSWLDNN GKSAVKKLKN SLPLRKELDR LKDELSHQLQ LSDIRWQRSW GIAHRCSQLH SLSRLAQQNL ETLKKAKGCT IIFTDRSGM SAVGHVMLGT MDVHHHWTKL FERLPSYFDL QRRLMILEDQ ISYLLGGIQV VYIEELQPVL TLEEYYSLLD V FYNRLLKS ...String:
TTLTSWLDNN GKSAVKKLKN SLPLRKELDR LKDELSHQLQ LSDIRWQRSW GIAHRCSQLH SLSRLAQQNL ETLKKAKGCT IIFTDRSGM SAVGHVMLGT MDVHHHWTKL FERLPSYFDL QRRLMILEDQ ISYLLGGIQV VYIEELQPVL TLEEYYSLLD V FYNRLLKS RILFHPRSLR GLQMILNSDR YAPSLHELGH FNIPTLCDPA NLQWFILTKA QQARENMKRK EELKVIENEL IQ ASTKKFS LEKLYKEPSI SSIQMVDCCK RLLEQSLPYL HGMHLCISHF YSVMQDGDLC IPWNW

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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
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1342786
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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