3JD0

Glutamate dehydrogenase in complex with GTP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase.

Borgnia, M.J.Banerjee, S.Merk, A.Matthies, D.Bartesaghi, A.Rao, P.Pierson, J.Earl, L.A.Falconieri, V.Subramaniam, S.Milne, J.L.

(2016) Mol.Pharmacol. 89: 645-651

  • DOI: 10.1124/mol.116.103382
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cryo-electron microscopy (cryo-EM) methods are now being used to determine structures at near-atomic resolution and have great promise in molecular pharmacology, especially in the context of mapping the binding of small-molecule ligands to protein co ...

    Cryo-electron microscopy (cryo-EM) methods are now being used to determine structures at near-atomic resolution and have great promise in molecular pharmacology, especially in the context of mapping the binding of small-molecule ligands to protein complexes that display conformational flexibility. We illustrate this here using glutamate dehydrogenase (GDH), a 336-kDa metabolic enzyme that catalyzes the oxidative deamination of glutamate. Dysregulation of GDH leads to a variety of metabolic and neurologic disorders. Here, we report near-atomic resolution cryo-EM structures, at resolutions ranging from 3.2 Å to 3.6 Å for GDH complexes, including complexes for which crystal structures are not available. We show that the binding of the coenzyme NADH alone or in concert with GTP results in a binary mixture in which the enzyme is in either an "open" or "closed" state. Whereas the structure of NADH in the active site is similar between the open and closed states, it is unexpectedly different at the regulatory site. Our studies thus demonstrate that even in instances when there is considerable structural information available from X-ray crystallography, cryo-EM methods can provide useful complementary insights into regulatory mechanisms for dynamic protein complexes.


    Organizational Affiliation

    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (M.J.B., S.B., A.M., D.M., A.B., P.R., L.A.E., V.F., S.S., J.L.S.M.) and FEI Company, Hillsboro, Oregon (J.P.).,Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland (M.J.B., S.B., A.M., D.M., A.B., P.R., L.A.E., V.F., S.S., J.L.S.M.) and FEI Company, Hillsboro, Oregon (J.P.) ss1@nih.gov jmilne@mail.nih.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate dehydrogenase 1, mitochondrial
A, B, C, D, E, F
501Bos taurusMutation(s): 0 
Gene Names: GLUD1 (GLUD)
EC: 1.4.1.3
Find proteins for P00366 (Bos taurus)
Go to Gene View: GLUD1
Go to UniProtKB:  P00366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-11
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Data collection