8XCS

Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus in complex with NADPH, AKG and NH4 in the initial stage of reaction

• PDB DOI: https://doi.org/10.2210/pdb8XCS/pdb
• EM Map EMD-38253: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Thermococcus profundus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-10 Released: 2023-12-27 
• Deposition Author(s): Wakabayashi, T., Oide, M., Nakasako, M.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Science and Technology

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.63 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase

Wakabayashi, T., Oide, M., Nakasako, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 47.67 kDa 
• Atom Count: 3,360 
• Modelled Residue Count: 418 
• Deposited Residue Count: 419 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A	419	Thermococcus profundus	Mutation(s): 0  Gene Names: gdhA EC: 1.4.1.3
UniProt
Find proteins for O74024 (Thermococcus profundus) Explore O74024  Go to UniProtKB:  O74024

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP (Subject of Investigation/LOI)	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
AKG (Subject of Investigation/LOI)	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
NH4 (Subject of Investigation/LOI)	D [auth A]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.63 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	4.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Wakabayashi, T., Oide, M., Nakasako, M.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	jp13480214
Japan Society for the Promotion of Science (JSPS)	Japan	jp19204042
Japan Society for the Promotion of Science (JSPS)	Japan	jp22244054
Japan Society for the Promotion of Science (JSPS)	Japan	jp21H01050
Japan Society for the Promotion of Science (JSPS)	Japan	jp26800227
Japan Society for the Promotion of Science (JSPS)	Japan	jp18J11653
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp15076210
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp20050030
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp22018027
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp23120525
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp25120725
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp15H01647
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp17H05891
Japan Science and Technology	Japan	JPMJPR22E2

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release