Fig. 4: Interactions between the LD and the catalytic domain of E2.

a The putative scheme of the substrate channeling mechanism in the catalytic cycle of PDHc, as shown in Fig. 1f. The diagram highlights the second step of the catalytic cycle, emphasizing the interactions between the LD and the PDHc core in the second step of PDHc catalytic cycle. b 4.3 Å resolution sub-tomogram average structure of the E2/E3BP core (grey) fitting with our PDHc core atomic structure (green, PDB: 9j1w). The transparent density shows one E2/E3BP trimer with a lower threshold. The additional density indicated by the red arrow represents the extension from the PDHc core. The extended densities were classified into two classes shown in (c, d). c One class average show E2 trimer density, which has no significant extended density and fits well with the E2 trimer (PDB: 9j1w). d The other class average with extended densities on the E2 trimer, which fits well with the E2-LD model predicted by AlphaFold2 (Supplementary Fig. 6c). e The interaction interface between the LD and E2 trimer, corresponding to the structure shown in (d) with a rotation to better visualize the active site region. f Enlarged view of the dash framed region in (e), which shows the interaction interface between the LD and E2 trimer. The dihydrolipoamide (DHLA) was placed in the active site channel based on our cryo-EM SPA resolved PDHc core structure (Supplementary Fig. 4b–d). g The electrostatic surface potential map of the E2-LD interaction interface. The key amino acids involved in the interaction was analyzed by MD simulations and shown in different colors. h Frequency distribution of the interactions between K259 of LD and residues of E2. Residues where the frequency exceeds 40% in all repetitions of MD simulations were marked with red stars, while those exceeding 40% in part of repetitions were marked with black stars. The names of residues and bars are colored according to their polarity. LD: lipoyl domain, S: PSBD.