Fig. 8: ColabFold predictions identify SWSN-7 and SWSN-6 as potential MAB-9 interactors.
From: Cell type-specific functions of the PBAF chromatin-remodeling complex in neuronal diversification
a ColabFold confidence metrics of predicted structures for MAB-9 and SWSN-7, and MAB-9 and SWSN-6 complexes, with 5 models generated for each pairwise interaction. pTM (red) and ipTM (blue) values for the 5 top-ranked structures for each complex are plotted. pTM: predicted template modelling—confidence of overall complex prediction. ipTM: interface predicted template modelling—confidence of relative subunit placement. Gray dashed line: 0.3 ipTM cutoff determined as warranting future investigation71. b Predicted Alignment Error plots for 5 top ranked models of MAB-9 and SWSN-7, and MAB-9 and SWSN-6, complexes. Heat map color corresponds to expected positional error at a residue in angstroms. Within a plot, top left represents MAB-9 monomer confidence, bottom right represents SWSN-7 (top row) or SWSN-6 (bottom row) monomer confidence, and off-diagonal boxes represent placement confidence of residues between subunits (interaction confidence). c Structural visualization of the top-ranked MAB-9/SWSN-7 complex prediction. Light orange: MAB-9. Dark orange: MAB-9 DNA binding domain (DBD). Blue: SWSN-7. Magenta dashed lines: inter-chain polar contacts predicted by PyMOL. Inset: zoomed in view of the interface region highlighting polar contacts. Side-chains involved in polar contacts shown as licorice-sticks. d Structural visualization of the top-ranked MAB-9/SWSN-6 complex prediction. Light orange: MAB-9. Dark orange: MAB-9 DNA binding domain (DBD). Blue: SWSN-6. Magenta dashed lines: inter-chain polar contacts predicted by PyMOL. Inset: zoomed in view of the interface region highlighting polar contacts. Side-chains involved in polar contacts shown as licorice-sticks. e Western blots (anti-HA) of co-immunoprecipitation (co-IP) experiments in HEK293 cells show binding between MAB-9 and both SWSN-6 and SWSN-7. Left: Western blot shows presence of MAB-9::HA in protein lysate when SWSN-6::3XFLAG and SWSN-7::3XFLAG are pulled down. Right: Western blot shows presence of SWSN-6::HA and SWSN-7::HA in protein lysate when MAB-9::Myc is pulled down. Red asterisks indicate target protein in pulldown lanes. Negative controls (lanes 5–8) show an absence of target protein in pulldown lanes. Negative controls include: (1) MAB-9::HA or MAB-9::Myc co-transfected with pcDNA3.1_3xFLAG::BAP (BAP: bacterial alkaline phosphatase) and (2) pcDNA3.1_3xFLAG::BAP alone. Bottom: Western blots show beta-Actin protein loading control. These reciprocal co-IP experiments were repeated once. Source data are provided as a Source Data file.
