The researchers combined data on the size, shape, structure, and neighbors of every NPC protein to create a set of positional probabilities, or “restraints,” which were then analyzed and optimized to produce a final structure. Rout compared it in principle to solving a crossword puzzle, in which partial knowledge of one word restrains the possibilities for many others. “If you have tens of thousands of these restraints,” he says, “you can pare down until a protein is restrained to a volume of its own size.”
Previous characterizations of the NPC structure did not resolve the positions of its individual components. Nine years of work went into the generation and analysis of the data, although future studies of other cell structures should be faster.
The new structure is highly symmetrical. “It's very clear that the underlying architecture of the NPC is modular,” says Rout, “and likely arose from several rounds of gene duplication.” Each column is paired with an adjacent one of related proteins; the pairs give rise to eight identical spokes that make up the NPC. Gene duplication may also have given rise to the prominent inner and outer rings, which circle within the NPC like concentric belts.
The structure is not the last word on the subject; it gives a protein-level but not atomic-level picture. It also does not include the fine structure of the basket, which projects into the cytoplasm and is believed to aid nuclear transport. The team is now working on solving these structures.