Extended Data Fig. 2: Assembly intermediates and complexes of PFD and PFDL subunits identified across DIP–MS experiments.
From: DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes
Across the PFDN2 (n = 3 biologically independent experiments) and UXT (biological replicates: n = 3 biologically independent experiments) DIP–MS assemblies we characterized 7 distinct coelution peak groups of PFD, PFDL, R2TP and CCT/TRiC core-subunits. The canonical PFD complex and PDRG1 eluted at Fraction 58 with an apparent MW of 157 kDa (coelution group 1) and the PFDL-module eluted at Fraction 37 with an apparent MW of 522 kDa (coelution group 2). The R2TP subassembly (coelution group 3 or Fraction 32 apparent MW 643 kDa) and the two adaptor peak subassemblies (apparent MW 356 kDa and 721 kDa or Fraction 45 and 29 assigned as coelution group 4 and 5) were recovered within both DIP-MS experiments. The larger assemblies, CCT/TRiC-Prefoldin (coelution group 6, apparent MW 804 kDa or Fraction 26) and the PAQosome (coelution group 7, apparent MW of 1015 kDa Fraction 19) are indicated at the bottom. Shared subunits and shared complex modules are indicated by arrows and boxes. Below the subassembly, the apparent MW derived from the separation is indicated. Sub-complex stoichiometry was inferred from literature reported assemblies. Apparent MW calibration curve data is in Supplementary Data 1. Within the DIP-MS of UXT the PFD and PFD-CCT/TRiC was not recovered (only residual CCT/TRiC from background). For the coelution groups profile plots, the y-axis represents the average MS2 protein intensities normalized by the maximum protein intensity across the gel slices (x-axis).
