Molecular architecture of the mammalian 2-oxoglutarate dehydrogenase complex

• Published in: Nature communications Vol. 15; no. 1; pp. 8407 - 15
• Main Authors: Zhang, Yitang, Chen, Maofei, Chen, Xudong, Zhang, Minghui, Yin, Jian, Yang, Zi, Gao, Xin, Zhang, Sensen, Yang, Maojun
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 27.09.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 101/28; 631/45/607/1167; 631/45/612/1240; 631/535/1258/1259; 631/535/1258/1260; Animals; Assembly; Cryoelectron Microscopy; Dehydrogenase; Dehydrogenases; Electron Microscope Tomography; Electron microscopy; Humanities and Social Sciences; Ketoglutarate Dehydrogenase Complex - chemistry; Ketoglutarate Dehydrogenase Complex - metabolism; Ketoglutaric acid; Models, Molecular; Molecular structure; multidisciplinary; Myocardium - enzymology; Myocardium - metabolism; Oxoglutarate dehydrogenase (lipoamide); Protein Subunits - chemistry; Protein Subunits - metabolism; Science; Science (multidisciplinary); Sus scrofa; Tricarboxylic acid cycle
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-52792-7

The 2-oxoglutarate dehydrogenase complex (OGDHc) orchestrates a critical reaction regulating the TCA cycle. Although the structure of each OGDHc subunit has been solved, the architecture of the intact complex and inter-subunit interactions still remain unknown. Here we report the assembly of native, intact OGDHc from Sus scrofa heart tissue using cryo-electron microscopy (cryo-EM), cryo-electron tomography (cryo-ET), and subtomogram averaging (STA) to discern native structures of the whole complex and each subunit. Our cryo-EM analyses revealed the E2o cubic core structure comprising eight homotrimers at 3.3-Å resolution. More importantly, the numbers, positions and orientations of each OGDHc subunit were determined by cryo-ET and the STA structures of the core were resolved at 7.9-Å with the peripheral subunits reaching nanometer resolution. Although the distribution of the peripheral subunits E1o and E3 vary among complexes, they demonstrate a certain regularity within the position and orientation. Moreover, we analyzed and validated the interactions between each subunit, and determined the flexible binding mode for E1o, E2o and E3, resulting in a proposed model of Sus scrofa OGDHc. Together, our results reveal distinctive factors driving the architecture of the intact, native OGDHc. The 2-oxoglutarate dehydrogenase complex (OGDHc) is a rate-limiting enzyme complex regulating the TCA cycle. Here, the authors use cryo-EM and cryo-ET to discern native structures of the whole complex and reveal its assembly mechanism.