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Yorodumi- PDB-7wgr: Cryo-electron microscopic structure of the 2-oxoglutarate dehydro... -
+Open data
-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 | ||||||
Components | 2-oxoglutarate dehydrogenase, mitochondrialOxoglutarate dehydrogenase complex | ||||||
Keywords | OXIDOREDUCTASE / Mitochondria / ketoglutarate dehydrogenase / single-particle cryoEM | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å | ||||||
Authors | Yu, X. / Yang, W. / Zhong, Y.H. / Ma, X.M. / Gao, Y.Z. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wgr.cif.gz | 306.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wgr.ent.gz | 250.4 KB | Display | PDB format |
PDBx/mmJSON format | 7wgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/7wgr ftp://data.pdbj.org/pub/pdb/validation_reports/wg/7wgr | HTTPS FTP |
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-Related structure data
Related structure data | 32485MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Homo sapiens (human) / Gene: OGDH / Production host: Escherichia coli (E. coli) 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 |
-Sample preparation
Component | Name: 2-oxoglutarate dehydrogenase, OGDHOxoglutarate dehydrogenase complex Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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) |
-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 | ||||||||||||||||||||||||
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