Metabolon-embedded pyruvate dehydrogenase complex E2 core at near-atomic resolution

Experimental Data Snapshot

  • Resolution: 3.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Cryo-EM snapshots of a native lysate provide structural insights into a metabolon-embedded transacetylase reaction.

Tuting, C.Kyrilis, F.L.Muller, J.Sorokina, M.Skalidis, I.Hamdi, F.Sadian, Y.Kastritis, P.L.

(2021) Nat Commun 12: 6933-6933

  • DOI: https://doi.org/10.1038/s41467-021-27287-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Found across all kingdoms of life, 2-keto acid dehydrogenase complexes possess prominent metabolic roles and form major regulatory sites. Although their component structures are known, their higher-order organization is highly heterogeneous, not only across species or tissues but also even within a single cell. Here, we report a cryo-EM structure of the fully active Chaetomium thermophilum pyruvate dehydrogenase complex (PDHc) core scaffold at 3.85 Å resolution (FSC = 0.143) from native cell extracts. By combining cryo-EM with macromolecular docking and molecular dynamics simulations, we resolve all PDHc core scaffold interfaces and dissect the residing transacetylase reaction. Electrostatics attract the lipoyl domain to the transacetylase active site and stabilize the coenzyme A, while apolar interactions position the lipoate in its binding cleft. Our results have direct implications on the structural determinants of the transacetylase reaction and the role of flexible regions in the context of the overall 10 MDa PDHc metabolon architecture.

  • Organizational Affiliation

    Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyltransferase component of pyruvate dehydrogenase complex459Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Find proteins for G0S4X6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S4X6 
Go to UniProtKB:  G0S4X6
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UniProt GroupG0S4X6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

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Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Database references
  • Version 1.2: 2024-07-17
    Changes: Data collection, Derived calculations, Refinement description