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TitleCryo-EM and artificial intelligence visualize endogenous protein community members.
Journal, issue, pagesStructure, Vol. 30, Issue 4, Page 575-589.e6, Year 2022
Publish dateApr 7, 2022
AuthorsIoannis Skalidis / Fotis L Kyrilis / Christian Tüting / Farzad Hamdi / Grzegorz Chojnowski / Panagiotis L Kastritis /
PubMed AbstractCellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and ...Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and thioesters of coenzyme-A synthesis. Metabolons are highly heterogeneous due to their function, making their analysis particularly challenging. Here, we simultaneously characterize metabolon-embedded architectures of a 60S pre-ribosome, fatty acid synthase, and pyruvate/oxoglutarate dehydrogenase complex E2 cores de novo. Cryo-electron microscopy (cryo-EM) 3D reconstructions are resolved at 3.84-4.52 Å resolution by collecting <3,000 micrographs of a single cellular fraction. After combining cryo-EM with artificial intelligence-based atomic modeling and de novo sequence identification methods, at this resolution range, polypeptide hydrogen bonding patterns are discernible. Residing molecular components resemble their purified counterparts from other eukaryotes but also exhibit substantial conformational variation with potential functional implications. Our results propose an integrated tool, boosted by machine learning, that opens doors for structural systems biology spearheaded by cryo-EM characterization of native cell extracts.
External linksStructure / PubMed:35093201
MethodsEM (single particle)
Resolution3.84 - 4.52 Å
Structure data

EMDB-13093:
Immature 60S Ribosomal Subunit from C. thermophilum
Method: EM (single particle) / Resolution: 4.52 Å

13844

7q5q

EMDB-13844, PDB-7q5q:
Protein community member oxoglutarate dehydrogenase complex E2 core from C. thermophilum
Method: EM (single particle) / Resolution: 4.38 Å

13845

7q5r

EMDB-13845, PDB-7q5r:
Protein community member pyruvate dehydrogenase complex E2 core from C. thermophilum
Method: EM (single particle) / Resolution: 3.84 Å

13846

7q5s

EMDB-13846, PDB-7q5s:
Protein community member fatty acid synthase complex from C. thermophilum
Method: EM (single particle) / Resolution: 4.47 Å

Source
  • chaetomium thermophilum var. thermophilum dsm 1495 (fungus)
  • chaetomium thermophilum (strain dsm 1495 / cbs 144.50 / imi 039719) (fungus)
KeywordsTRANSFERASE / Dihydrolipoyl Succinyltransferase / E2 / Oxoglutarate / a-Ketoglutarate / Dihydrolipoyl / transacetylase / Pyruvate / Fatty Acid Synthase / complex / chaetomium / thermophilum / fatty / acid / synthesis

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