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- EMDB-32485: Cryo-electron microscopic structure of the 2-oxoglutarate dehydro... -

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Basic information

Entry
Database: EMDB / ID: EMD-32485
TitleCryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) component of the human alpha-ketoglutarate (2-oxoglutarate) dehydrogenase complex
Map data
Sample
  • Complex: 2-oxoglutarate dehydrogenase, OGDHOxoglutarate dehydrogenase complex
    • Protein or peptide: 2-oxoglutarate dehydrogenase, mitochondrialOxoglutarate dehydrogenase complex
  • Ligand: CALCIUM IONCalcium
  • Ligand: MAGNESIUM ION
  • Ligand: THIAMINE DIPHOSPHATEThiamine pyrophosphate
Function / homology
Function and homology information


oxoglutarate dehydrogenase (NAD+) activity / olfactory bulb mitral cell layer development / oxoglutarate dehydrogenase (succinyl-transferring) / succinyl-CoA metabolic process / : / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / tangential migration from the subventricular zone to the olfactory bulb / Lysine catabolism / cerebellar cortex development ...oxoglutarate dehydrogenase (NAD+) activity / olfactory bulb mitral cell layer development / oxoglutarate dehydrogenase (succinyl-transferring) / succinyl-CoA metabolic process / : / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / tangential migration from the subventricular zone to the olfactory bulb / Lysine catabolism / cerebellar cortex development / pyramidal neuron development / Citric acid cycle (TCA cycle) / thalamus development / 2-oxoglutarate metabolic process / striatum development / Glyoxylate metabolism and glycine degradation / thiamine pyrophosphate binding / tricarboxylic acid cycle / generation of precursor metabolites and energy / hippocampus development / mitochondrial membrane / glycolytic process / mitochondrial matrix / mitochondrion / metal ion binding / nucleus
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsYu X / Yang W / Zhong YH / Ma XM / Gao YZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural basis for the activity and regulation of human alpha-ketoglutarate dehydrogenase revealed by Cryo-EM
Authors: Zhong Y / Gao Y / Zhou D / Ma X / Chen H / Xu Y / Yang W / Yu X
History
DepositionDec 28, 2021-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateJun 1, 2022-
Current statusJun 1, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32485.png

Downloads & links

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Map

FileDownload / File: emd_32485.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.845 Å
Density
Contour LevelBy AUTHOR: 0.143
Minimum - Maximum-1.5640783 - 2.3120975
Average (Standard dev.)-0.0017839812 (±0.07656639)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 216.32 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

EntireName: 2-oxoglutarate dehydrogenase, OGDHOxoglutarate dehydrogenase complex
Components
  • Complex: 2-oxoglutarate dehydrogenase, OGDHOxoglutarate dehydrogenase complex
    • Protein or peptide: 2-oxoglutarate dehydrogenase, mitochondrialOxoglutarate dehydrogenase complex
  • Ligand: CALCIUM IONCalcium
  • Ligand: MAGNESIUM ION
  • Ligand: THIAMINE DIPHOSPHATEThiamine pyrophosphate

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Supramolecule #1: 2-oxoglutarate dehydrogenase, OGDH

SupramoleculeName: 2-oxoglutarate dehydrogenase, OGDH / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: 2-oxoglutarate dehydrogenase, mitochondrial

MacromoleculeName: 2-oxoglutarate dehydrogenase, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: oxoglutarate dehydrogenase (succinyl-transferring)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102.006258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AVQSLIRAYQ IRGHHVAQLD PLGILDADLD SSVPADIISS TDKLGFYGLD ESDLDKVFHL PTTTFIGGQE SALPLREIIR RLEMAYCQH IGVEFMFIND LEQCQWIRQK FETPGIMQFT NEEKRTLLAR LVRSTRFEEF LQRKWSSEKR FGLEGCEVLI P ALKTIIDK ...String:
AVQSLIRAYQ IRGHHVAQLD PLGILDADLD SSVPADIISS TDKLGFYGLD ESDLDKVFHL PTTTFIGGQE SALPLREIIR RLEMAYCQH IGVEFMFIND LEQCQWIRQK FETPGIMQFT NEEKRTLLAR LVRSTRFEEF LQRKWSSEKR FGLEGCEVLI P ALKTIIDK SSENGVDYVI MGMPHRGRLN VLANVIRKEL EQIFCQFDSK LEAADEGSGD VKYHLGMYHR RINRVTDRNI TL SLVANPS HLEAADPVVM GKTKAEQFYC GDTEGKKVMS ILLHGDAAFA GQGIVYETFH LSDLPSYTTH GTVHVVVNNQ IGF TTDPRM ARSSPYPTDV ARVVNAPIFH VNSDDPEAVM YVCKVAAEWR STFHKDVVVD LVCYRRNGHN EMDEPMFTQP LMYK QIRKQ KPVLQKYAEL LVSQGVVNQP EYEEEISKYD KICEEAFARS KDEKILHIKH WLDSPWPGFF TLDGQPRSMS CPSTG LTED ILTHIGNVAS SVPVENFTIH GGLSRILKTR GEMVKNRTVD WALAEYMAFG SLLKEGIHIR LSGQDVERGT FSHRHH VLH DQNVDKRTCI PMNHLWPNQA PYTVCNSSLS EYGVLGFELG FAMASPNALV LWEAQFGDFH NTAQCIIDQF ICPGQAK WV RQNGIVLLLP HGMEGMGPEH SSARPERFLQ MCNDDPDVLP DLKEANFDIN QLYDCNWVVV NCSTPGNFFH VLRRQILL P FRKPLIIFTP KSLLRHPEAR SSFDEMLPGT HFQRVIPEDG PAAQNPENVK RLLFCTGKVY YDLTRERKAR DMVGQVAIT RIEQLSPFPF DLLLKEVQKY PNAELAWCQE EHKNQGYYDY VKPRLRTTIS RAKPVWYAGR DPAAAPATGN KKTHLTELQR LLDTAFDLD VFKNFS

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: THIAMINE DIPHOSPHATE

MacromoleculeName: THIAMINE DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: TPP
Molecular weightTheoretical: 425.314 Da
Chemical component information

ChemComp-TPP:
THIAMINE DIPHOSPHATE / Thiamine pyrophosphate

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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

Concentration1.5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 266798

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