9N4V

Azotobacter vinelandii extended type VI secretion system sheath tube complex

Summary for 9N4V

• Entry DOI: 10.2210/pdb9n4v/pdb
• EMDB information: 48906
• Descriptor: DUF877 family protein, Type VI secretion system contractile sheath small subunit (3 entities in total)
• Functional Keywords: secretion system, transport protein
• Biological source: Azotobacter vinelandii; More
• Total number of polymer chains: 48
• Total formula weight: 1821163.42

Authors

Warmack, R.A. (deposition date: 2025-02-03, release date: 2025-07-16, Last modification date: 2025-09-17)

Primary citation

Shen, Y.,Maggiolo, A.O.,Zhang, T.,Warmack, R.A.
CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes.
Structure, 33:1484-, 2025

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.

PubMed: 40664216
DOI: 10.1016/j.str.2025.06.007

Experimental method

ELECTRON MICROSCOPY (1.85 Å)