6JNA

Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo-electron microscopy.

Oide, M.Kato, T.Oroguchi, T.Nakasako, M.

(2020) Febs J. --: --

  • DOI: 10.1111/febs.15224
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Analysis of the conformational changes of protein is important to elucidate the mechanisms of protein motions correlating with their function. Here, we studied the spontaneous domain motion of unliganded glutamate dehydrogenase from Thermococcus prof ...

    Analysis of the conformational changes of protein is important to elucidate the mechanisms of protein motions correlating with their function. Here, we studied the spontaneous domain motion of unliganded glutamate dehydrogenase from Thermococcus profundus using cryo-electron microscopy and proposed a novel method to construct free-energy landscape of protein conformations. Each subunit of the homo-hexameric enzyme comprises nucleotide-binding domain (NAD domain) and hexamer-forming core domain. A large active-site cleft is situated between the two domains and varies from open to close according to the motion of a NAD domain. A three-dimensional map reconstructed from all cryo-electron microscopy images displayed disordered volumes of NAD domains, suggesting that NAD domains in the collected images adopted various conformations in domain motion. Focused classifications on NAD domain of subunits provided several maps of possible conformations in domain motion. To deduce what kinds of conformations appeared in EM images, we developed a novel analysis method that describe the EM maps as a linear combination of representative conformations appearing in a 200-ns molecular dynamics simulation as reference. The analysis enabled us to estimate the appearance frequencies of the representative conformations, which illustrated a free-energy landscape in domain motion. In the open/close domain motion, two free-energy basins hindered the direct transformation from open to closed state. Structure models constructed for representative EM maps in classifications demonstrated the correlation between the energy landscape and conformations in domain motion. Based on the results, the domain motion in glutamate dehydrogenase and the analysis method to visualize conformational changes and free-energy landscape were discussed. DATABASE: The EM maps of the four conformations were deposited to Electron Microscopy Data Bank (EMDB) as accession codes EMD-9845 (open), EMD-9846 (half-open1), EMD-9847 (half-open2), and EMD-9848 (closed), respectively. In addition, the structural models built for the four conformations were deposited to the Protein Data Bank (PDB) as accession codes 6JN9 (open), 6JNA (half-open1), 6JNC (half-open2), and 6JND (closed), respectively.


    Organizational Affiliation

    RIKEN SPring-8 Center, Sayo-gun, Japan.,Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate dehydrogenase
A
419Thermococcus profundusMutation(s): 0 
Gene Names: gdhA (gdh)
EC: 1.4.1.3
Find proteins for O74024 (Thermococcus profundus)
Go to UniProtKB:  O74024
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
phenix.real_space_refinerefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanjp13480214
Japan Society for the Promotion of ScienceJapanjp19204042
Japan Society for the Promotion of ScienceJapanjp22244054
Japan Society for the Promotion of ScienceJapanjp26800227
Japan Society for the Promotion of ScienceJapanjp17H04854
Japan Society for the Promotion of ScienceJapan18J11653
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp15076210
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp20050030
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp22018027
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp23120525
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp25120725
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp15H01647
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp17H05891
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp26104535

Revision History 

  • Version 1.0: 2020-02-12
    Type: Initial release