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- EMDB-38452: Structure of the native 2-oxoglutarate dehydrogenase complex (OGD... -

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Basic information

Entry
Database: EMDB / ID: EMD-38452
TitleStructure of the native 2-oxoglutarate dehydrogenase complex (OGDHC) in the adult cortex and hippocampus
Map data
Sample
  • Complex: Mammalian OGDHC from rat brain
    • Protein or peptide: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial
Keywords2-oxoglutarate dehydrogenase complex (OGDHC) / 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 / oxoadipate dehydrogenase complex / L-lysine catabolic process to acetyl-CoA via saccharopine / succinyl-CoA metabolic process / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex ...Glycine degradation / OGDH complex synthesizes succinyl-CoA from 2-OG / Protein lipoylation / OADH complex synthesizes glutaryl-CoA from 2-OA / oxoadipate dehydrogenase complex / 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 / : / acyltransferase activity / tricarboxylic acid cycle / heat shock protein binding / protein-folding chaperone binding / 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 speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhang M / Feng J / Li Y / Zhu S
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Cell / Year: 2025
Title: Assembly and architecture of endogenous NMDA receptors in adult cerebral cortex and hippocampus.
Authors: Ming Zhang / Juan Feng / Chun Xie / Nan Song / Chaozhi Jin / Jian Wang / Qun Zhao / Lihua Zhang / Boshuang Wang / Yidi Sun / Fei Guo / Yang Li / Shujia Zhu /
Abstract: The cerebral cortex and hippocampus are crucial brain regions for learning and memory, which depend on activity-induced synaptic plasticity involving N-methyl-ᴅ-aspartate receptors (NMDARs). ...The cerebral cortex and hippocampus are crucial brain regions for learning and memory, which depend on activity-induced synaptic plasticity involving N-methyl-ᴅ-aspartate receptors (NMDARs). However, subunit assembly and molecular architecture of endogenous NMDARs (eNMDARs) in the brain remain elusive. Using conformation- and subunit-dependent antibodies, we purified eNMDARs from adult rat cerebral cortex and hippocampus. Three major subtypes of GluN1-N2A-N2B, GluN1-N2B, and GluN1-N2A eNMDARs were resolved by cryoelectron microscopy (cryo-EM) at the resolution up to 4.2 Å. The particle ratio of these three subtypes was 9:7:4, indicating that about half of GluN2A and GluN2B subunits are incorporated into the tri-heterotetramers. Structural analysis revealed the asymmetric architecture of the GluN1-N2A-N2B receptor throughout the extracellular to the transmembrane layers. Moreover, the conformational variations between GluN1-N2B and GluN1-N2A-N2B receptors revealed the distinct biophysical properties across different eNMDAR subtypes. Our findings imply the structural and functional complexity of eNMDARs and shed light on structure-based therapeutic design targeting these eNMDARs in vivo.
History
DepositionDec 26, 2023-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38452.png

Downloads & links

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Map

FileDownload / File: emd_38452.map.gz / Format: CCP4 / Size: 303.3 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.)
1.07 Å/pix.
x 430 pix.
= 460.53 Å		1.07 Å/pix.
x 430 pix.
= 460.53 Å		1.07 Å/pix.
x 430 pix.
= 460.53 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.288
Minimum - Maximum-0.9332667 - 1.418375
Average (Standard dev.)0.0005567981 (±0.033522394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions430430430
Spacing430430430
CellA=B=C: 460.53 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38452_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_38452_half_map_1.map
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Half map: #1

Fileemd_38452_half_map_2.map
Projections & Slices
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Sample components

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Entire : Mammalian OGDHC from rat brain

EntireName: Mammalian OGDHC from rat brain
Components
  • Complex: Mammalian OGDHC from rat brain
    • Protein or peptide: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial

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Supramolecule #1: Mammalian OGDHC from rat brain

SupramoleculeName: Mammalian OGDHC from rat brain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

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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: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 23.953686 KDa
SequenceString: LKEAQNTCAM LTTFNEVDMS NIQEMRARHK DAFLKKHNLK LGFMSAFVKA SAFALQEQPV VNAVIDDATK EVVYRDYIDI SVAVATPRG LVVPVIRNVE TMNYADIERT INELGEKARK NELAIEDMDG GTFTISNGGV FGSLFGTPII NPPQSAILGM H GIFDRPVA ...String:
LKEAQNTCAM LTTFNEVDMS NIQEMRARHK DAFLKKHNLK LGFMSAFVKA SAFALQEQPV VNAVIDDATK EVVYRDYIDI SVAVATPRG LVVPVIRNVE TMNYADIERT INELGEKARK NELAIEDMDG GTFTISNGGV FGSLFGTPII NPPQSAILGM H GIFDRPVA VGGKVEVRPM MYVALTYDHR LIDGREAVTF LRKIKAAVED PRVLLLDL

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 statetissue

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-10 (5k 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: 2.5 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 268960
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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