Piecing Together the Nuclear Pore Complex
February 2015
Scientists are exploring larger and larger molecular machines by combining the many tools of integrative structural biology. The nuclear pore complex has been a subject of this study for many years, revealing an increasingly detailed view. It is a challenging subject for many reasons: it is highly dynamic as it performs its duty of transporting molecules in and out of the nucleus, and by molecular standards, it is huge, comprised of over 450 protein subunits. The complex has been studied extensively by electron microscopy, revealing a characteristic eight-fold symmetric ring crossing the nuclear membrane (shown here from entry EMD-2444 at the EMDataResource). More recently, researchers are determining the atomic structures of the individual components, and using them to reconstruct the whole complex.
Flexible Nucleoporins
PSI researchers at NYSGRC have recently determined the structure of Nup192, a nucleoporin protein that forms part of the inner ring of the nuclear pore complex. The structure reveals a protein that folds into three domains, each composed of a collection of alpha helices, shown here from PDB entry 4ifq. Several lines of evidence reveal that the protein is quite flexible, including SAXS and EM studies of the isolated protein and molecular dynamics computations on the structure. This motion may help the nuclear pore complex flex to accommodate cargo of different sizes as they pass through the pore.
Nup192 Reconstruction
As is often the case with flexible proteins, PSI researchers needed to use a divide-and-conquer approach with this nucleoporin. They determined the atomic structure of half of the protein, and combined this with electron microscopy to reconstruct a model for the entire protein. A 3D tomographic reconstruction of the protein, shown here from entry EMD-5556 at the EMDataResource, reveals a long structure shaped like a question mark. The atomic structure fits nicely into the hook-shaped end of the reconstruction.
Distant Cousins
Comparison of the Nup192 structure revealed a possible evolutionary relationship to other proteins involved in cellular trafficking. As we might expect, the yeast Nup192 structure solved by PSI researchers is quite similar to a recent structure of fungal Nup192, PDB entry 4knh. More distant relatives, which all show a similar pattern of alpha-helical domains, include karyopherins such as Kap-alpha shown here (PDB entry 1ee4), as well as beta-catenin and adaptor protein 1. To explore these structures in more detail, the JSmol tab below displays an interactive JSmol.
Nup192 and Relatives (PDB entries 4ifq, 4knh, 1ee4, 1ibr, 1qz7 & 1w63)
Two structures of Nup192 and several structurally related proteins are overlapped here. Notice the similar folding pattern comprised of alpha-helical domains. Use the buttons to switch between the proteins and change the representation.
References
4knh: Stuwe, T., Lin, D. H., Collins, L. N., Hurt, E. & Hoelz, A. Evidence for an evolutionary relationship between the large adaptor protein Nup192 and karyopherins. Proc. Natl. Acad. Sci. USA 111, 2530-2535 (2014).
4ifq: Sampathkumar, P., et al. Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex. Structure 21, 560-571 (2013).
Bui, K. H., et al. Integrated structural analysis of the human nuclear pore complex scaffold. Cell 155, 1233-1243 (2013).
Heldwein, E. et al. Crystal structure of the clathrin adaptor protein 1 core. Proc. Natl. Acad. Sci. USA 101, 14108-14113 (2004).
1qz7: Xing, Y, Clements, W. K., Kimelman, D. & Xu, W. Crystal structure of a beta- catenin/axin complex suggests a mechanism for the beta-catenin destruction complex. Genes Dev. 17, 2753-2764 (2003).
1ee4: Conti, E. & Kuriyan, J. Crystallographic analysis of the specific yet versatile recognition of distinct nuclear localization signals by karyopherin alpha. Structure Fold. Des. 8, 329-338 (2000).
Vetter, I. R., Arndt, A., Kutay, U., Gorlich, D. & Wittinghofer, A. Structural view of the Ran-importin beta interaction at 2.3 A resolution. Cell 97, 635-646 (1999).
