Molecule of the Month: Nuclear Pore Complex

Bacterial cells are built for speed, but our cells are built for complexity. Because we have so many types of cells, with so many different functions, our cells need more levels of regulation than bacteria. To achieve this, our cells separate the process of protein synthesis into two compartments: DNA is transcribed to mRNA in the nucleus, while mRNA is translated to protein in the cytoplasm. This separation allows additional regulatory steps to be added to the process, such as capping and splicing of the mRNA. The nuclear pore complex (NPC), a huge channel embedded in the nuclear envelope, connects these two separated processes, providing two-way transport of nucleic acids and proteins between the nucleus and cytoplasm.

The NPC is a huge molecular complex composed of hundreds of nucleoporin proteins. The symmetric core structure is composed of two outer rings that provide support and an inner ring that forms the transport channel. Other less symmetric structures manage molecules on both sides of the pore. The entire structure can transport about 1,000 molecules every second, ranging from proteins to entire ribosomal subunits.

Because the structure of the entire NPC is so large and dynamic, a “divide-and-conquer” approach has been used to study it. Atomic-resolution crystal structures of single nucleoporins and their subcomplexes have been determined individually, and maps of the entire NPC scaffold, detailed enough to see proteins but not individual atoms, have been determined using electron microscopy. This information has been integrated by docking the atomic structures into the electron density maps to elucidate the overall structure. The illustration included here combines two of these integrative structures to give a view of the core infrastructure of the pore, including the outer ring from PDB entry 5a9q and the inner channel ring from PDB entry 5ijn.

The diffusion channel at the center of the NPC controls passage of molecules between the nucleus and cytoplasm. Small molecules can freely pass through the pore, but large molecules need to be actively transported. Transport proteins, called karyopherins, interact with unstructured nucleoporin chains that extend into the transport channel, as seen in PDB entry 5dis. They bind to a phenylalanine-glycine sequence that is repeated many times along the nucleoporin chain. Through transient interactions with these FG repeats, karyopherins migrate through the channel, taking their cargo with them.