9N4X | pdb_00009n4x

CryoEM structure of the Azotobacter vinelandii glutamine synthetase

  • Classification: LIGASE
  • Organism(s): Azotobacter vinelandii DJ
  • Mutation(s): No 

  • Deposited: 2025-02-03 Released: 2025-07-30 
  • Deposition Author(s): Warmack, R.A., Shen, Y.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes.

Shen, Y.Maggiolo, A.O.Zhang, T.Warmack, R.A.

(2025) Structure 

  • DOI: https://doi.org/10.1016/j.str.2025.06.007
  • Primary Citation of Related Structures:  
    9N4V, 9N4W, 9N4X, 9N4Y, 9N59, 9N5A, 9NSV

  • PubMed Abstract: 

    Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry and machine learning, they promise to facilitate the visual exploration of proteomes. Leveraging visual proteomics, we interrogate structures isolated from a complex cellular milieu by cryoEM to identify and classify molecular structures and complexes de novo. By comparing three automated model building programs, CryoID, DeepTracer, and ModelAngelo, we determine the identity of six distinct oligomeric protein complexes from partially purified extracts of the nitrogen-fixing bacterium Azotobacter vinelandii using both anaerobic and aerobic cryoEM, including two original oligomeric structures. Overall, by allowing the study of near-native oligomeric protein states, cryoEM-enabled visual proteomics reveals unique structures that correspond to relevant species observed in situ.


  • Organizational Affiliation
    • Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA 91125, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine synthetase467Azotobacter vinelandii DJMutation(s): 0 
EC: 6.3.1.2
UniProt
Find proteins for P22248 (Azotobacter vinelandii)
Explore P22248 
Go to UniProtKB:  P22248
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22248
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC4.4

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM143836
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM152765

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release