7WGR

Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) component of the human alpha-ketoglutarate (2-oxoglutarate) dehydrogenase complex

• PDB DOI: https://doi.org/10.2210/pdb7WGR/pdb
• EM Map EMD-32485: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-12-28 Released: 2022-06-01 
• Deposition Author(s): Yu, X., Yang, W., Zhong, Y.H., Ma, X.M., Gao, Y.Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for the activity and regulation of human alpha-ketoglutarate dehydrogenase revealed by Cryo-EM

Zhong, Y., Gao, Y., Zhou, D., Ma, X., Chen, H., Xu, Y., Yang, W., Yu, X.

(2022) Biochem Biophys Res Commun 602: 120-126

• DOI: https://doi.org/10.1016/j.bbrc.2022.02.093

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 204.99 kDa 
• Atom Count: 13,614 
• Modelled Residue Count: 1,700 
• Deposited Residue Count: 1,790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoglutarate dehydrogenase, mitochondrial	A, B	895	Homo sapiens	Mutation(s): 0  Gene Names: OGDH EC: 1.2.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02218 (Homo sapiens) Explore Q02218  Go to UniProtKB:  Q02218
PHAROS:  Q02218 GTEx:  ENSG00000105953

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP (Subject of Investigation/LOI)	E [auth A], H [auth B]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
CA (Subject of Investigation/LOI)	C [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Yu, X., Yang, W., Zhong, Y.H., Ma, X.M., Gao, Y.Z.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2024-06-26
  Changes: Data collection