Simulated structurally variable Nuclear Pore Complexes for Microscopy simulations

The Nuclear Pore Complex (NPC) is a massive, 8-fold symmetrical protein assembly that enables macromolecular exchange between the cytoplasm and nucleus. The average architecture of proteins within the NPC has been resolved with pseudo-atomic precision, however observed NPC heterogeneities such as varying diameters, elongated shapes, 9-fold symmetry, and irregular shapes evidence a high degree of divergence from this average. Single Molecule Localization Microscopy (SMLM) images NPCs at protein-level resolution, whereupon image analysis software studies their heterogeneity. Antithetically, NPCs have been used as a reference standard for SMLM due to their abundance, size, and symmetry. Ground truth annotations would ultimately aid both lines of research, however SMLM noise impedes such annotations and complicates image analysis. This dataset therefore contains simulations of structurally variable NPCs based on an architectural model of the NPC (10.2210/pdb5A9Q/pdb). N-terminal coordinates of the NPC protein Nup107 have been manipulated to represent geometric variability in radius, height, internal twist, and elongation. Additionally, we represent the NPC as a spring-model such that arbitrary deforming forces simulate irregularly shaped variations of increasing magnitudes. The resulting coordinate data can be forwarded to SMLM simulation software, or to other microscopy simulation software.