Revealing the Nuclear Pore Complex

March 2012

This is an exciting time for the study of the nuclear pore complex, the highway of transport between the cytoplasm and nucleus, and also a central player in nuclear organization and gene regulation. Decades of electron micrographic work are now being combined with atomic structures to reveal the inner workings of this huge protein complex. With the help of PSI member NYSGRC, researchers have built comprehensive maps that bring together diverse data on the nuclear pore complex: proteomics studies provide a recipe of components; biophysical studies, such as sedimentation analysis and affinity purification, can reveal the shape of individual nucleoporin proteins and their interactions; and electron microscopy provides the overall ultrastructure, which when combined with specific antibodies provides the localization of proteins.

Symmetrical Structure

The map reveals a modular structure, built in several layers from 456 protein chains. In the middle, a ring of three types of proteins surrounds the central channel filled with tangled chains that guide cargo transport through the nuclear pore complex. This ring is anchored to the membrane by a complex scaffolding of proteins. Attached to this scaffold, a complex basket controls the flow of molecules on the nuclear side and long filaments guide molecules on the cytoplasmic side (not shown in the diagram). Surprisingly, the whole thing, one of the largest protein structures in the cell, is constructed of only about 30 types of proteins, but with many copies of each type.

Sequence Similarities

By analysis of the sequences of these nucleoporin proteins, researchers predicted that they actually share many common features, which were later confirmed by high-resolution analyses. Almost all fall into three classes: extended girders composed of many stacked alpha helices, small disk-shaped proteins composed of a propeller arrangement of beta sheets, and a specialized protein sequence that doesn't fold into any shape at all. The alpha helical proteins and propellers are sturdy folds for building the infrastructure of the nuclear pore complex. The unstructured chains, on the other hand, are perfect for displaying short recognition sequences that capture transport proteins and guide them through the central channel.

Nucleoporin Structures

As with many other complex biological structures, researchers are studying the structure of the nuclear pore complex by breaking it into parts. One large structural building block is shown here, termed the Nup84 complex, which assembles to form a ring that shapes the nuclear pore complex. It is particularly stable and amenable to study. The overall structure has been determined by electron microscopy, and many of the individual components have been studied by x-ray crystallography. Several structures are shown here, from PDB entries 3iko, 3ewe, 3f7f, 3kfo, 3kep, 3kfo, 1xip, 3i5p, 3nf5 and 2aiv. The proteins are colored to highlight the types of domains: the alpha-helical domains are in blue, and the propellers are in green. Researchers have also begun to map specific functions to particular parts of this complex, for instance, the two short arms seem to be particularly important for connecting this complex to the rest of the nuclear pore complex.

Structural Similarities

By looking at the sequences and structures of nucleoporins, researchers working with NYSGRC have discovered a similarity with other structural proteins. In particular, several of the scaffolding nucleoporins are very similiar to proteins that form geodesic coats around vesicles, such as clathrin, CopI and CopII, suggesting that these systems evolved from a similar ancestor. This makes sense because the alpha-helical fold is highly modular, and can be modified through gene duplication to form a variety of structures with different lengths. To compare the structure of a CopII protein and several nucleoporins, the JSmol tab below displays an interactive JSmol.

Sec31 and Nucleoporins (PDB entries 2pm6, 2qx5, 3f3f, and 3iko)

Sec31 protein from CopII and several nucleoporins share a common folding motif composed of many stacked alpha helices. When looking at these proteins, notice that the core structure is similar, forming a rod-shaped infrastructure, which is then decorated with loops and tails that interact with their different partners. Use the buttons to view the different proteins and change the representation.

Sec31   Nic96   Nup85   Nup84   Nup145C  

Representation show backbone   show ribbons   show atoms  


  1. Devos, D., et al. Simple fold composition and modular architecture of the nuclear pore complex. Proc. Natl. Acad. Sci. USA 103, 2172-2177 (2006).

  2. Alber, F., et al. The molecular architecture of the nuclear pore complex. Nature 450, 695-701 (2007).

  3. Brohawn, S. G., Partridge, J. R., Whittle, J. R. R. & Schwartz, T. U. The nuclear pore complex has entered the atomic age. Structure 17, 1156-1168 (2009).

  4. Hoelz, A., Debler, E. W. & Blobel, G. The structure of the nuclear pore complex. Ann. Rev. Biochem. 80, 613-643 (2011).

  5. Fernandez-Martinez, J., et al. Structure-function mapping of a heptameric module in the nuclear pore complex. J. Cell. Biol. in press.