Cryo-EM structure of glutamate dehydrogenase at 1.8 A resolution

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery.

Merk, A.Bartesaghi, A.Banerjee, S.Falconieri, V.Rao, P.Davis, M.I.Pragani, R.Boxer, M.B.Earl, L.A.Milne, J.L.Subramaniam, S.

(2016) Cell 165: 1698-1707

  • DOI: https://doi.org/10.1016/j.cell.2016.05.040
  • Primary Citation of Related Structures:  
    5K0Z, 5K10, 5K11, 5K12

  • PubMed Abstract: 

    Recent advances in single-particle cryoelecton microscopy (cryo-EM) are enabling generation of numerous near-atomic resolution structures for well-ordered protein complexes with sizes ≥ ∼200 kDa. Whether cryo-EM methods are equally useful for high-resolution structural analysis of smaller, dynamic protein complexes such as those involved in cellular metabolism remains an important question. Here, we present 3.8 Å resolution cryo-EM structures of the cancer target isocitrate dehydrogenase (93 kDa) and identify the nature of conformational changes induced by binding of the allosteric small-molecule inhibitor ML309. We also report 2.8-Å- and 1.8-Å-resolution structures of lactate dehydrogenase (145 kDa) and glutamate dehydrogenase (334 kDa), respectively. With these results, two perceived barriers in single-particle cryo-EM are overcome: (1) crossing 2 Å resolution and (2) obtaining structures of proteins with sizes < 100 kDa, demonstrating that cryo-EM can be used to investigate a broad spectrum of drug-target interactions and dynamic conformational states.

  • Organizational Affiliation

    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate dehydrogenase 1, mitochondrial
A, B, C, D, E
A, B, C, D, E, F
558Bos taurusMutation(s): 0 
Find proteins for P00366 (Bos taurus)
Explore P00366 
Go to UniProtKB:  P00366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00366
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references
  • Version 1.2: 2016-11-23
    Changes: Other
  • Version 1.3: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references, Refinement description