Extended Data Fig. 3: Systematic fitting of Y complex and Inner Ring complex into the human DLD-1 map.
From: The cellular environment shapes the nuclear pore complex architecture
a, Fitting of the Cytoplasmic Ring Y complex with the previous NPC model (PDB: 5A9Q) compared with our composite model. The details of this fitting are provided in the Methods section. All fitting runs were performed using Chimera with 1,000,000 random initial placements and local cross-correlation (Chimera’s correlation about the mean, CAM), or a combination of local cross-correlation and overlap (CAM+OVR) for scoring. For each model, the top scoring model is shown to the left of a histogram of raw scores. The top scoring model is indicated on the histogram (red arrowhead) with its associated adjusted p-value for two different scoring metrics tested (red text represents the fit identified in the histogram, black represents the alternate metric). Two-sided P-values were corrected for multiple testing using the Benjamini-Hochberg procedure. The resulting composite Y model underwent an additional local optimization step to further improve the density fit (black arrowheads indicate regions that are improved with this step). An overlay of our model and the previous model is also shown in the panel. b, Same as a, but for the Nuclear Ring Y complex, also starting with PDB 5A9Q. c, Overlay of our composite Y complex model with that of the previous model. The additional modeled regions in our Y complex model “hub” (Nup160, 85, 96 and Sec13) and are indicated (blue arrowheads). d, Fitting of the Inner Ring complex with the previous IR model (PDB: 5IJN) compared with our model. e, Overlay of our modified IR complex model with the previous model.
