Determining the architectures of macromolecular assemblies

Nature

Volumn 450, Issue 7170, 2007, Pages 683-694

  Alber, Frank ^a   Dokudovskaya, Svetlana ^b,c   Veenhoff, Liesbeth M ^b,d   Zhang, Wenzhu ^b   Kipper, Julia ^b,e   Devos, Damien ^a,f   Suprapto, Adisetyantari ^b   Karni Schmidt, Orit ^b,g   Williams, Rosemary ^b   Chait, Brian T ^b   Rout, Michael P ^b   Sali, Andrej ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b ROCKEFELLER UNIVERSITY   (United States)

^c INSTITUT JACQUES MONOD   (France)

^d UNIVERSITY OF GRONINGEN   (Netherlands)

^e GERMAN AEROSPACE CENTER DLR   (Germany)

^f EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^g Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

CYTOLOGY; MOLECULAR ANALYSIS; PROTEOMICS;

ANALYTIC METHOD; ARTICLE; DATA ANALYSIS; INFORMATION PROCESSING; MACROMOLECULE; NUCLEAR PORE COMPLEX; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTEOMICS;

EID: 36749088906     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature06404     Document Type: Article

References (45)

1. Sali, A., Glaeser, R., Earnest, T. & Baumeister, W. From words to literature in structural proteomics. Nature 422, 216-225 (2003).
2. Rout, M. P. et al. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148, 635-651 (2000).
3. Macara, I. G. Transport into and out of the nucleus. Microbiol. Mol. Biol. Rev. 65, 570-594 (2001).
4. Weis, K. Nucleocytoplasmic transport: cargo trafficking across the border. Curr. Opin. Cell Biol. 14, 328-335 (2002).
5. Yang, Q., Rout, M. P. & Akey, C. W. Three-dimensional architecture of the isolated yeast nuclear pore complex: functional and evolutionary implications. Mol. Cell 1, 223-234 (1998).
6. Beck, M., Lucic, V., Förster, F., Baumeister, E. & Medalia, O. Snapshots of nuclear pore complexes in action captured by cryo-electron tomography. Nature 449, 611-615 (2007).
7. Devos, D. et al. Simple fold composition and modular architecture of the nuclear pore complex. Proc. Natl Acad. Sci. USA 103, 2172-2177 (2006).
8. Havel, T. F. & Wüthrich, K. A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of intramolecular 1H-1H proximities in solution. Bull. Math. Biol. 46, 673-698 (1984).
9. Malhotra, A., Tan, R. K. & Harvey, S. C. Prediction of the three-dimensional structure of Escherichia coli 30S ribosomal subunit: a molecular mechanics approach. Proc. Natl Acad. Sci. USA 87, 1950-1954 (1990).
10. Denning, D. P., Patel, S. S., Uversky, V., Fink, A. L. & Rexach, M. Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded. Proc. Natl Acad. Sci. USA 100, 2450-2455 (2003).
11. Lim, R. Y. et al. Flexible phenylalanine-glycine nucleoporins as entropic barriers to nucleocytoplasmic transport. Proc. Natl Acad. Sci. USA 103, 9512-9517 (2006).
12. Devos, D. et al. Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PLoS Biol. 2, e380 (2004).
13. Siniossoglou, S. et al. Structure and assembly of the Nup84p complex. J. Cell Biol. 149, 41-54 (2000).
14. Lutzmann, M., Kunze, R., Buerer, A., Aebi, U. & Hurt, E. Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins. EMBO J. 21, 387-397 (2002).
15. Strambio-de-Castillia, C., Blobel, G. & Rout, M. P. Isolation and characterization of nuclear envelopes from the Yeast Saccharomyces. J. Cell Biol. 131, 19-31 (1995).
16. Miller, A. L. et al. Cytoplasmic inositol hexakisphosphate production is sufficient for mediating the Gle1-mRNA export pathway. J. Biol. Chem. 279, 51022-51032 (2004).
17. Solsbacher, J., Maurer, P., Vogel, F. & Schlenstedt, G. Nup2p, a yeast nucleoporin, functions in bidirectional transport of importin alpha. Mol. Cell. Biol. 20, 8468-8479 (2000).
18. Marelli, M., Aitchison, J. D. & Wozniak, R. W. Specific binding of the karyopherin Kap121p to a subunit of the nuclear pore complex containing Nup53p, Nup59p, and Nup170p. J. Cell Biol. 143, 1813-1830 (1998).
19. Archambault, V. et al. Genetic and biochemical evaluation of the importance of Cdc6 in regulating mitotic exit. Mol. Biol. Cell 14, 4592-4604 (2003).
20. Archambault, V. et al. Targeted proteomic study of the cyclin-Cdk module. Mol. Cell 14, 699-711 (2004).
21. Tackett, A. J. et al. I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions. J. Proteome Res. 4, 1752-1756 (2005).
22. Cristea, I. M., Williams, R., Chait, B. T. & Rout, M. P. Fluorescent proteins as proteomic probes. Mol. Cell. Proteomics 4, 1933-1941 (2005).
23. Niepel, M., Strambio-de-Castillia, C., Fasolo, J., Chait, B. T. & Rout, M. P. The nuclear pore complex-associated protein, Mlp2p, binds to the yeast spindle pole body and promotes its efficient assembly. J. Cell Biol. 170, 225-235 (2005).
24. Cristea, I. M. et al. Tracking and elucidating alphavirus-host protein interactions. J. Biol. Chem. 281, 30269-30278 (2006).
25. Zhang, W. & Chait, B. T. ProFound: an expert system for protein identification using mass spectrometric peptide mapping information. Anal. Chem. 72, 2482-2489 (2000).
26. Krutchinsky, A. N., Kalkum, M. & Chait, B. T. Automatic identification of proteins with a MALDI-quadrupole ion trap mass spectrometer. Anal. Chem. 73, 5066-5077 (2001).
27. Stelter, P. et al. Molecular basis for the functional interaction of dynein light chain with the nuclear-pore complex. Nature Cell Biol. 9, 788-796 (2007).
28. Murphy, R., Watkins, J. L. & Wente, S. R. GLE2, a Saccharomyces cerevisiae homologue of the Schizosaccharomyces pombe export factor RAE1, is required for nuclear pore complex structure and function. Mol. Biol. Cell 7, 1921-1937 (1996).
29. Murphy, R. & Wente, S. R. An RNA-export mediator with an essential nuclear export signal. Nature 383, 357-360 (1996).
30. Lutzmann, M. et al. Reconstitution of Nup157 and Nup145N into the Nup84 complex. J. Biol. Chem. 280, 18442-18451 (2005).
31. Bailer, S. M. et al. Nup116p associates with the Nup82p-Nsp1p-Nup159p nucleoporin complex. J. Biol. Chem. 275, 2354-23548 (2000).
32. Grandi, P., Doye, V. & Hurt, E. C. Purification of NSP1 reveals complex formation with 'GLFG' nucleoporins and a novel nuclear pore protein NIC96. EMBO. J. 12, 3061-3071 (1993).
33. Shen, M. Y. & Sali, A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 15, 2507-2524 (2006).
34. Harding, S. E. Determination of macromolecular homogeneity, shape, and interactions using sedimentation velocity analytical ultracentrifugation. Methods Mol. Biol. 22, 61-73 (1994).
35. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567-580 (2001).
36. Alber, F., Kim, M. F. & Sali, A. Structural characterization of assemblies from overall shape and subcomplex compositions. Structure 13, 435-445 (2005).
37. Alber, F. et al. The molecular architecture of the nuclear pore complex. Nature doi:10.1038/nature06405 (this issue).
38. Akey, C. W. & Radermacher, M. Architecture of the Xenopus nuclear pore complex revealed by three-dimensional cryo-electron microscopy. J. Cell Biol. 122, 1-19 (1993).
39. Stoffler, D. et al. Cryo-electron tomography provides novel insights into nuclear pore architecture: implications for nucleocytoplasmic transport. J. Mol. Biol. 328, 119-130 (2003).
40. Kiseleva, E. et al. Yeast nuclear pore complexes have a cytoplasmic ring and internal filaments. J. Struct. Biol. 145, 272-288 (2004).
41. Hinshaw, J. E., Carragher, B. O. & Milligan, R. A. Architecture and design of the nuclear pore complex. Cell 69, 1133-1141 (1992).
42. Beck, M. et al. Nuclear pore complex structure and dynamics revealed by cryoelectron tomography. Science 306, 1387-1390 (2004).
43. Pante, N. & Kann, M. Nuclear pore complex is able to transport macromolecules with diameters of about 39 nm. Mol. Biol. Cell 13, 425-434 (2002).
44. Drin, G. et al. A general amphipathic α-helical motif for sensing membrane curvature. Nature Struct. Mol. Biol. 14, 138-146 (2007).
45. Schurmann, G., Haspel, J., Grumet, M. & Erickson, H. P. Cell adhesion molecule L1 in folded (horseshoe) and extended conformations. Mol. Biol. Cell 12, 1765-1773 (2001).