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- PDB-7wgr: Cryo-electron microscopic structure of the 2-oxoglutarate dehydro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wgr | ||||||
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Title | Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) component of the human alpha-ketoglutarate (2-oxoglutarate) dehydrogenase complex | ||||||
![]() | 2-oxoglutarate dehydrogenase, mitochondrial | ||||||
![]() | OXIDOREDUCTASE / Mitochondria / ketoglutarate dehydrogenase / single-particle cryoEM | ||||||
Function / homology | ![]() oxoglutarate dehydrogenase (NAD+) activity / olfactory bulb mitral cell layer development / oxoglutarate dehydrogenase (succinyl-transferring) / : / succinyl-CoA metabolic process / oxoglutarate dehydrogenase (succinyl-transferring) activity / tangential migration from the subventricular zone to the olfactory bulb / cerebellar cortex development / Lysine catabolism / oxoglutarate dehydrogenase complex ...oxoglutarate dehydrogenase (NAD+) activity / olfactory bulb mitral cell layer development / oxoglutarate dehydrogenase (succinyl-transferring) / : / succinyl-CoA metabolic process / oxoglutarate dehydrogenase (succinyl-transferring) activity / tangential migration from the subventricular zone to the olfactory bulb / cerebellar cortex development / Lysine catabolism / oxoglutarate dehydrogenase complex / 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 / Mitochondrial protein degradation / generation of precursor metabolites and energy / mitochondrial membrane / hippocampus development / glycolytic process / mitochondrial matrix / mitochondrion / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å | ||||||
![]() | Yu, X. / Yang, W. / Zhong, Y.H. / Ma, X.M. / Gao, Y.Z. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 312.2 KB | Display | ![]() |
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PDB format | ![]() | 245.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 47.1 KB | Display | |
Data in CIF | ![]() | 72.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 32485MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 102006.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q02218, oxoglutarate dehydrogenase (succinyl-transferring) #2: Chemical | #3: Chemical | #4: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 2-oxoglutarate dehydrogenase, OGDH / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 266798 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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