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Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex

Nature Structural & Molecular Biology volume 16, pages 782–788 (2009)Cite this article

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Abstract

The nuclear pore complex mediates nucleocytoplasmic transport in all eukaryotes and is among the largest cellular assemblies of proteins, collectively known as nucleoporins. Nucleoporins are organized into distinct subcomplexes. We optimized the isolation of a putative membrane-coating subcomplex of the nuclear pore complex, the heptameric Nup84 complex, and analyzed its structure by EM. Our data confirmed the previously reported 'Y' shape. We discerned additional structural details, including specific hinge regions at which the particle shows great flexibility. We determined the three-dimensional structures of two conformers, mapped the localization of two nucleoporins within the subcomplex and docked known crystal structures into the EM maps. The free ends of the Y-shaped particle are formed by β-propellers; the connecting segments consist of α-solenoids. Notably, the same organizational principle is found in the clathrin triskelion, which may share a common evolutionary origin with the heptameric complex.

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Figure 1: Purification and EM of the heptameric Nup84 complex.
Figure 2: Alignment, classification and averaging of particle images reveals structural details of the heptameric complex.
Figure 3: Heterogeneity of particle appearance.
Figure 4: Three-dimensional structures of the heptameric complex.
Figure 5: Mapping of nucleoporin localization.
Figure 6: Protein arrangement within the heptameric complex.

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  • 14 June 2009

    In the version of the supplementary information originally posted online, the captions for the Supplementary Movies were in the incorrect order. This has been corrected as of 14 June 2009.

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Acknowledgements

We thank R. Diaz-Avalos, W. Rice and other staff at the New York Structural Biology Center for their support and stimulating discussions; D. King (Howard Hughes Medical Institute Mass Spectrometry Facility) for MS; E. Debler, V. Nagy, C. Atkinson and A. Mattheyses for critical reading of the manuscript; and D. Andor, K.-C. Hsia and other members of the Blobel laboratory for helpful discussions. M.K. was supported by the Howard Hughes Medical Institute Predoctoral Fellowship.

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Authors and Affiliations

  1. Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA

    Martin Kampmann & Günter Blobel

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  1. Martin Kampmann
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  2. Günter Blobel
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Correspondence to Günter Blobel.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 and Supplementary Discussion (PDF 10037 kb)

Supplementary Movie 1

Overlay of final map 1 (orange) and map 1 reconstructed from the 25% best matching particles (purple), see Supplementary Discussion. (MOV 3846 kb)

Supplementary Movie 2

Overlay of final map 2 (orange) and map 2 reconstructed from the 25% best matching particles (purple), see Supplementary Discussion. (MOV 3858 kb)

Supplementary Movie 3

Crystal structures docked into map 1. The color code is the same as in Figure 6. (MOV 2028 kb)

Supplementary Movie 4

Crystal structures docked into map 2. The color code is the same as in Figure 6. (MOV 1992 kb)

Supplementary Movie 5

Crystal structures docked into map 2, detail. Blue and red spheres mark the N and C termini, respectively, which belong to crystal structures of partial proteins, in order to indicate were the protein domains that are absent from the crystal structure would originate. (MOV 2947 kb)

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Kampmann, M., Blobel, G. Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex. Nat Struct Mol Biol 16, 782–788 (2009). https://doi.org/10.1038/nsmb.1618

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