8EW0

Cryo-EM structure of glutamate dehydrogenase frozen at various temperature

  • Classification: LYASE
  • Organism(s): Bos taurus
  • Mutation(s): No 

  • Deposited: 2022-10-21 Released: 2023-01-11 
  • Deposition Author(s): Shi, H., Wu, C., Zhang, X.
  • Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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

Addressing compressive deformation of proteins embedded in crystalline ice.

Shi, H.Wu, C.Zhang, X.

(2023) Structure 31: 213

  • DOI: https://doi.org/10.1016/j.str.2022.12.001
  • Primary Citation of Related Structures:  
    8BQN, 8EW0, 8EW2, 8F49, 8F7Y, 8HHS, 8HI2

  • PubMed Abstract: 

    For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. Whether and how crystalline ice affects single-particle cryo-EM is still unclear. Here, single-particle cryo-EM was used to analyze three-dimensional structures of various proteins and viruses embedded in crystalline ice formed at various cooling rates. Low cooling rates led to shrinkage deformation and density distortions on samples having loose structures. Higher cooling rates reduced deformations. Deformation-free proteins in crystalline ice were obtained by modifying the freezing conditions, and reconstructions from these samples revealed a marked improvement over vitreous ice. This procedure also increased the efficiency of cryo-EM structure determinations and was essential for high-resolution reconstructions.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China.


Macromolecules
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 
EC: 1.4.1.3
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31930069

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection