EMD-61084

Subtomogram averaging
6.9 Å
EMD-61084 Deposition: 05/08/2024
Map released: 05/02/2025
Last modified: 05/02/2025
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-61084

The conformation of lipoy domain binding the core of the pyruvate dehydrogenase complex.

EMD-61084

Subtomogram averaging
6.9 Å
EMD-61084 Deposition: 05/08/2024
Map released: 05/02/2025
Last modified: 05/02/2025
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Sus scrofa
Sample: The conformation of LD binding the core of the pyruvate dehydrogenase complex.

Deposition Authors: Wang C , Chang YJ , Zhang X
Dynamics of the mammalian pyruvate dehydrogenase complex revealed by in-situ structural analysis.
Wang C , Ma C , Xu Y, Chang S, Wu H, Yan C, Chen J, Wu Y, An S, Xu J, Han Q, Jiang Y, Jiang Z, Chu X, Gao H , Zhang X , Chang Y
(2025) Nat Commun , 16 , 917 - 917
PUBMED: 39843418
DOI: doi:10.1038/s41467-025-56171-8
ISSN: 2041-1723
Abstract:
The multi-enzyme pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle and plays vital roles in metabolism, energy production, and cellular signaling. Although all components have been individually characterized, the intact PDHc structure remains unclear, hampering our understanding of its composition and dynamical catalytic mechanisms. Here, we report the in-situ architecture of intact mammalian PDHc by cryo-electron tomography. The organization of peripheral E1 and E3 components varies substantially among the observed PDHcs, with an average of 21 E1 surrounding each PDHc core, and up to 12 E3 locating primarily along the pentagonal openings. In addition, we observed dynamic interactions of the substrate translocating lipoyl domains (LDs) with both E1 and E2, and the interaction interfaces were further analyzed by molecular dynamics simulations. By revealing intrinsic dynamics of PDHc peripheral compositions, our findings indicate a distinctive activity regulation mechanism, through which the number of E1, E3 and functional LDs may be coordinated to meet constantly changing demands of metabolism.