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TitleCryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes.
Journal, issue, pagesStructure, Vol. 33, Issue 9, Page 1484-11497.e5, Year 2025
Publish dateSep 4, 2025
AuthorsYuanbo Shen / Ailiena O Maggiolo / Tianzheng Zhang / Rebeccah A Warmack /
PubMed AbstractSingle particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry ...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.
External linksStructure / PubMed:40664216 / PubMed Central
MethodsEM (helical sym.) / EM (single particle)
Resolution1.85 - 3.7 Å
Structure data

48906

9n4v

EMDB-48906, PDB-9n4v:
Azotobacter vinelandii extended type VI secretion system sheath tube complex
Method: EM (helical sym.) / Resolution: 1.85 Å

48907

9n4w

EMDB-48907, PDB-9n4w:
Decameric Glucose-6-phosphate isomerase from Azotobacter vinelandii
Method: EM (single particle) / Resolution: 2.5 Å

48914

9n4x

EMDB-48914, PDB-9n4x:
CryoEM structure of the Azotobacter vinelandii glutamine synthetase
Method: EM (single particle) / Resolution: 3.2 Å

48915

9n4y

EMDB-48915, PDB-9n4y:
CryoEM structure of a filamentous soluble pyridine nucleotide transhydrogenase
Method: EM (helical sym.) / Resolution: 3.7 Å

48918

9n59

EMDB-48918, PDB-9n59:
CryoEM structure of the Azotobacter vinelandii flagellar filament
Method: EM (helical sym.) / Resolution: 2.82 Å

48919

9n5a

EMDB-48919, PDB-9n5a:
CryoEM structure of Azotobacter vinelandii bacterioferritin
Method: EM (single particle) / Resolution: 2.96 Å

49753

9nsv

EMDB-49753, PDB-9nsv:
CryoEM structure of ancestral nitrogenase MoFe-protein
Method: EM (single particle) / Resolution: 2.19 Å

Chemicals

ChemComp-HOH:
WATER

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

ChemComp-ICS:
iron-sulfur-molybdenum cluster with interstitial carbon

ChemComp-HCA:
3-HYDROXY-3-CARBOXY-ADIPIC ACID

ChemComp-CLF:
FE(8)-S(7) CLUSTER

ChemComp-FE:
Unknown entry

Source
  • azotobacter vinelandii (bacteria)
KeywordsTRANSPORT PROTEIN / secretion system / ISOMERASE / Glycolysis / decamer / LIGASE / nitrogen metabolism / FLAVOPROTEIN / transhydrogenase / STRUCTURAL PROTEIN / Flagellum / METAL BINDING PROTEIN / Metal storage / OXIDOREDUCTASE / Metalloprotein

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