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Volumn 13, Issue 11, 2014, Pages 2927-2943

Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex

Author keywords

[No Author keywords available]

Indexed keywords

COATOMER PROTEIN; CROSS LINKING REAGENT; NUCLEOPORIN; NUP84 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 84910595462     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M114.041673     Document Type: Article
Times cited : (139)

References (91)
  • 4
    • 37249065351 scopus 로고    scopus 로고
    • The molecular sociology of the cell
    • Robinson, C. V., Sali, A., and Baumeister, W. (2007) The molecular sociology of the cell. Nature 450, 973-982
    • (2007) Nature , vol.450 , pp. 973-982
    • Robinson, C.V.1    Sali, A.2    Baumeister, W.3
  • 5
    • 48749103296 scopus 로고    scopus 로고
    • Integrating diverse data for structure determination of macromolecular assemblies
    • Alber, F., Forster, F., Korkin, D., Topf, M., and Sali, A. (2008) Integrating diverse data for structure determination of macromolecular assemblies. Annu. Rev. Biochem. 77, 443-477
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 443-477
    • Alber, F.1    Forster, F.2    Korkin, D.3    Topf, M.4    Sali, A.5
  • 6
    • 84874181173 scopus 로고    scopus 로고
    • Biochemistry. Integrative structural biology
    • Ward, A. B., Sali, A., and Wilson, I. A. (2013) Biochemistry. Integrative structural biology. Science 339, 913-915
    • (2013) Science , vol.339 , pp. 913-915
    • Ward, A.B.1    Sali, A.2    Wilson, I.A.3
  • 11
    • 84862917808 scopus 로고    scopus 로고
    • Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
    • Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F., and Chen, L. (2012) Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat. Biotechnol. 30, 90-98
    • (2012) Nat. Biotechnol. , vol.30 , pp. 90-98
    • Kalhor, R.1    Tjong, H.2    Jayathilaka, N.3    Alber, F.4    Chen, L.5
  • 17
    • 0034987721 scopus 로고    scopus 로고
    • Mass spectrometry as a tool for protein crystallography
    • Cohen, S. L., and Chait, B. T. (2001) Mass spectrometry as a tool for protein crystallography. Annu. Rev. Biophys. Biomol. Struct. 30, 67-85
    • (2001) Annu. Rev. Biophys. Biomol. Struct. , vol.30 , pp. 67-85
    • Cohen, S.L.1    Chait, B.T.2
  • 18
    • 0034705128 scopus 로고    scopus 로고
    • High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry
    • Young, M. M., Tang, N., Hempel, J. C., Oshiro, C. M., Taylor, E. W., Kuntz, I. D., Gibson, B. W., and Dollinger, G. (2000) High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 97, 5802-5806
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 5802-5806
    • Young, M.M.1    Tang, N.2    Hempel, J.C.3    Oshiro, C.M.4    Taylor, E.W.5    Kuntz, I.D.6    Gibson, B.W.7    Dollinger, G.8
  • 22
    • 33745742438 scopus 로고    scopus 로고
    • Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions
    • Sinz, A. (2006) Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom. Rev. 25, 663-682
    • (2006) Mass Spectrom. Rev. , vol.25 , pp. 663-682
    • Sinz, A.1
  • 25
    • 84875913034 scopus 로고    scopus 로고
    • Vivo protein interaction network identified with a novel real-time cross-linked peptide identification strategy
    • Weisbrod, C. R., Chavez, J. D., Eng, J. K., Yang, L., Zheng, C., and Bruce, J. E. (2013) In vivo protein interaction network identified with a novel real-time cross-linked peptide identification strategy. J. Proteome Res. 12, 1569-1579
    • (2013) J. Proteome Res. , vol.12 , pp. 1569-1579
    • Weisbrod, C.R.1    Chavez, J.D.2    Eng, J.K.3    Yang, L.4    Zheng, C.5    Bruce, J.E.6
  • 29
    • 0034695924 scopus 로고    scopus 로고
    • The yeast nuclear pore complex: Composition, architecture, and transport mechanism
    • Rout, A., Aitchison, J. D., Suprapto, A., Hjertaas, K., Zhao, Y., and Chait, B. T. (2000) The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 635-651
    • (2000) J. Cell Biol. , pp. 635-651
    • Rout, A.1    Aitchison, J.D.2    Suprapto, A.3    Hjertaas, K.4    Zhao, Y.5    Chait, B.T.6
  • 30
    • 0036469369 scopus 로고    scopus 로고
    • Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins
    • Lutzmann, M., Kunze, R., Buerer, A., Aebi, U., and Hurt, E. (2002) Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins. EMBO J. 21, 387-397
    • (2002) EMBO J. , vol.21 , pp. 387-397
    • Lutzmann, M.1    Kunze, R.2    Buerer, A.3    Aebi, U.4    Hurt, E.5
  • 31
    • 57149118232 scopus 로고    scopus 로고
    • Structural evidence for common ancestry of the nuclear pore complex and vesicle coats
    • Brohawn, S. G., Leksa, N. C., Spear, E. D., Rajashankar, K. R., and Schwartz, T. U. (2008) Structural evidence for common ancestry of the nuclear pore complex and vesicle coats. Science 322, 1369-1373
    • (2008) Science , vol.322 , pp. 1369-1373
    • Brohawn, S.G.1    Leksa, N.C.2    Spear, E.D.3    Rajashankar, K.R.4    Schwartz, T.U.5
  • 32
    • 9444273167 scopus 로고    scopus 로고
    • Components of coated vesicles and nuclear pore complexes share a common molecular architecture
    • Devos, D., Dokudovskaya, S., Alber, F., Williams, R., Chait, B. T., Sali, A., and Rout, M. P. (2004) Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PLoS Biol. 2, e380
    • (2004) PLoS Biol. , vol.2 , pp. e380
    • Devos, D.1    Dokudovskaya, S.2    Alber, F.3    Williams, R.4    Chait, B.T.5    Sali, A.6    Rout, M.P.7
  • 33
    • 84857690224 scopus 로고    scopus 로고
    • 3D ultrastructure of the nuclear pore complex
    • Bilokapic, S., and Schwartz, T. U. (2012) 3D ultrastructure of the nuclear pore complex. Curr. Opin. Cell Biol. 24, 86-91
    • (2012) Curr. Opin. Cell Biol. , vol.24 , pp. 86-91
    • Bilokapic, S.1    Schwartz, T.U.2
  • 34
    • 79959423595 scopus 로고    scopus 로고
    • The structure of the nuclear pore complex
    • Hoelz, A., Debler, E. W., and Blobel, G. (2011) The structure of the nuclear pore complex. Annu. Rev. Biochem. 80, 613-643
    • (2011) Annu. Rev. Biochem. , vol.80 , pp. 613-643
    • Hoelz, A.1    Debler, E.W.2    Blobel, G.3
  • 36
    • 67650318247 scopus 로고    scopus 로고
    • Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex
    • Kampmann, M., and Blobel, G. (2009) Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex. Nat. Struct. Mol. Biol. 16, 782-788
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 782-788
    • Kampmann, M.1    Blobel, G.2
  • 37
    • 84883489254 scopus 로고    scopus 로고
    • Protein interfaces of the conserved Nup84 complex from Chaetomium thermophilum shown by crosslinking mass spectrometry and electron microscopy
    • Thierbach, K., von Appen, A., Thoms, M., Beck, M., Flemming, D., and Hurt, E. (2013) Protein interfaces of the conserved Nup84 complex from Chaetomium thermophilum shown by crosslinking mass spectrometry and electron microscopy. Structure 21, 1672-1682
    • (2013) Structure , vol.21 , pp. 1672-1682
    • Thierbach, K.1    Von Appen, A.2    Thoms, M.3    Beck, M.4    Flemming, D.5    Hurt, E.6
  • 39
    • 34548336772 scopus 로고    scopus 로고
    • Higher-energy C-trap dissociation for peptide modification analysis
    • Olsen, J. V., Macek, B., Lange, O., Makarov, A., Horning, S., and Mann, M. (2007) Higher-energy C-trap dissociation for peptide modification analysis. Nat. Methods 4, 709-712
    • (2007) Nat. Methods , vol.4 , pp. 709-712
    • Olsen, J.V.1    Macek, B.2    Lange, O.3    Makarov, A.4    Horning, S.5    Mann, M.6
  • 41
    • 4644314911 scopus 로고
    • Preferential fragmentation of protonated gas-phase peptide ions adjacent to acidic amino-acid-residues
    • Qin, J., and Chait, B. T. (1995) Preferential fragmentation of protonated gas-phase peptide ions adjacent to acidic amino-acid-residues. J. Am. Chem. Soc. 117, 5411-5412
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5411-5412
    • Qin, J.1    Chait, B.T.2
  • 42
    • 84868332118 scopus 로고    scopus 로고
    • A systematic investigation into the nature of tryptic HCD spectra
    • Michalski, A., Neuhauser, N., Cox, J., and Mann, M. (2012) A systematic investigation into the nature of tryptic HCD spectra. J. Proteome Res. 11, 5479-5491
    • (2012) J. Proteome Res. , vol.11 , pp. 5479-5491
    • Michalski, A.1    Neuhauser, N.2    Cox, J.3    Mann, M.4
  • 44
    • 84856497340 scopus 로고    scopus 로고
    • Putting the pieces together: Integrative modeling platform software for structure determination of macromolecular assemblies
    • Russel, D., Lasker, K., Webb, B., Velazquez-Muriel, J., Tjioe, E., Schneidman-Duhovny, D., Peterson, B., and Sali, A. (2012) Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol. 10, e1001244
    • (2012) PLoS Biol. , vol.10 , pp. e1001244
    • Russel, D.1    Lasker, K.2    Webb, B.3    Velazquez-Muriel, J.4    Tjioe, E.5    Schneidman-Duhovny, D.6    Peterson, B.7    Sali, A.8
  • 45
    • 9444274034 scopus 로고    scopus 로고
    • Structural and functional analysis of Nup133 domains reveals modular building blocks of the nuclear pore complex
    • Berke, I. C., Boehmer, T., Blobel, G., and Schwartz, T. U. (2004) Structural and functional analysis of Nup133 domains reveals modular building blocks of the nuclear pore complex. J. Cell Biol. 167, 591-597
    • (2004) J. Cell Biol. , vol.167 , pp. 591-597
    • Berke, I.C.1    Boehmer, T.2    Blobel, G.3    Schwartz, T.U.4
  • 46
    • 69849086706 scopus 로고    scopus 로고
    • Architectural nucleoporins Nup157/170 and Nup133 are structurally related and descend from a second ancestral element
    • Whittle, J. R. R., and Schwartz, T. U. (2009) Architectural nucleoporins Nup157/170 and Nup133 are structurally related and descend from a second ancestral element. J. Biol. Chem. 284, 28442-28452
    • (2009) J. Biol. Chem. , vol.284 , pp. 28442-28452
    • Whittle, J.R.R.1    Schwartz, T.U.2
  • 47
    • 44949171609 scopus 로고    scopus 로고
    • Structural and functional studies of Nup107/Nup133 interaction and its implications for the architecture of the nuclear pore complex
    • Boehmer, T., Jeudy, S., Berke, I. C., and Schwartz, T. U. (2008) Structural and functional studies of Nup107/Nup133 interaction and its implications for the architecture of the nuclear pore complex. Mol. Cell 30, 721-731
    • (2008) Mol. Cell , vol.30 , pp. 721-731
    • Boehmer, T.1    Jeudy, S.2    Berke, I.C.3    Schwartz, T.U.4
  • 49
    • 70350755470 scopus 로고    scopus 로고
    • Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice
    • Brohawn, S. G., and Schwartz, T. U. (2009) Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice. Nat. Struct. Mol. Biol. 16, 1173-1177
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 1173-1177
    • Brohawn, S.G.1    Schwartz, T.U.2
  • 51
  • 52
    • 68149162580 scopus 로고    scopus 로고
    • The structure of the scaffold nucleoporin Nup120 reveals a new and unexpected domain architecture
    • Leksa, N. C., Brohawn, S. G., and Schwartz, T. U. (2009) The structure of the scaffold nucleoporin Nup120 reveals a new and unexpected domain architecture. Structure 17, 1082-1091
    • (2009) Structure , vol.17 , pp. 1082-1091
    • Leksa, N.C.1    Brohawn, S.G.2    Schwartz, T.U.3
  • 54
    • 34250745253 scopus 로고    scopus 로고
    • Structure and organization of coat proteins in the COPII cage
    • Fath, S., Mancias, J. D., Bi, X., and Goldberg, J. (2007) Structure and organization of coat proteins in the COPII cage. Cell 129, 1325-1336
    • (2007) Cell , vol.129 , pp. 1325-1336
    • Fath, S.1    Mancias, J.D.2    Bi, X.3    Goldberg, J.4
  • 55
    • 36849079742 scopus 로고    scopus 로고
    • Crystal structure of nucleoporin Nic96 reveals a novel, intricate helical domain architecture
    • Jeudy, S., and Schwartz, T. U. (2007) Crystal structure of nucleoporin Nic96 reveals a novel, intricate helical domain architecture. J. Biol. Chem. 282, 34904-34912
    • (2007) J. Biol. Chem. , vol.282 , pp. 34904-34912
    • Jeudy, S.1    Schwartz, T.U.2
  • 57
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding, J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21, 951-960
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 58
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Soding, J., Biegert, A., and Lupas, A. N. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33, W244-W248
    • (2005) Nucleic Acids Res. , vol.33 , pp. W244-W248
    • Soding, J.1    Biegert, A.2    Lupas, A.N.3
  • 59
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones, D. T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 62
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali, A., and Blundell, T. L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 64
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • Shen, M. Y., and Sali, A. (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci. 15, 2507-2524
    • (2006) Protein Sci. , vol.15 , pp. 2507-2524
    • Shen, M.Y.1    Sali, A.2
  • 66
    • 22144489530 scopus 로고    scopus 로고
    • Inferential structure determination
    • Rieping, W., Habeck, M., and Nilges, M. (2005) Inferential structure determination. Science 309, 303-306
    • (2005) Science , vol.309 , pp. 303-306
    • Rieping, W.1    Habeck, M.2    Nilges, M.3
  • 68
    • 0032729435 scopus 로고    scopus 로고
    • Exploring expression data: Identification and analysis of coexpressed genes
    • Heyer, L. J., Kruglyak, S., and Yooseph, S. (1999) Exploring expression data: identification and analysis of coexpressed genes. Genome Res. 9, 1106-1115
    • (1999) Genome Res. , vol.9 , pp. 1106-1115
    • Heyer, L.J.1    Kruglyak, S.2    Yooseph, S.3
  • 71
    • 84857966803 scopus 로고    scopus 로고
    • Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography
    • Leitner, A., Reischl, R., Walzthoeni, T., Herzog, F., Bohn, S., Forster, F., and Aebersold, R. (2012) Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Mol. Cell. Proteomics 11, M111.014126
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. M111-014126
    • Leitner, A.1    Reischl, R.2    Walzthoeni, T.3    Herzog, F.4    Bohn, S.5    Forster, F.6    Aebersold, R.7
  • 72
    • 84903715767 scopus 로고    scopus 로고
    • Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances
    • Merkley, E. D., Rysavy, S., Kahraman, A., Hafen, R. P., Daggett, V., and Adkins, J. N. (2014) Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances. Protein Sci. 23, 747-759
    • (2014) Protein Sci. , vol.23 , pp. 747-759
    • Merkley, E.D.1    Rysavy, S.2    Kahraman, A.3    Hafen, R.P.4    Daggett, V.5    Adkins, J.N.6
  • 73
    • 37349009269 scopus 로고    scopus 로고
    • Architecture of a coat for the nuclear pore membrane
    • Hsia, K. C., Stavropoulos, P., Blobel, G., and Hoelz, A. (2007) Architecture of a coat for the nuclear pore membrane. Cell 131, 1313-1326
    • (2007) Cell , vol.131 , pp. 1313-1326
    • Hsia, K.C.1    Stavropoulos, P.2    Blobel, G.3    Hoelz, A.4
  • 75
    • 0031604505 scopus 로고    scopus 로고
    • Three-dimensional architecture of the isolated yeast nuclear pore complex: Functional and evolutionary implications
    • Yang, Q., Rout, M. P., and Akey, C. W. (1998) Three-dimensional architecture of the isolated yeast nuclear pore complex: functional and evolutionary implications. Mol. Cell 1, 223-234
    • (1998) Mol. Cell , vol.1 , pp. 223-234
    • Yang, Q.1    Rout, M.P.2    Akey, C.W.3
  • 78
    • 77954310096 scopus 로고    scopus 로고
    • Structure of coatomer cage proteins and the relationship among COPI
    • Lee, C., and Goldberg, J. (2010) Structure of coatomer cage proteins and the relationship among COPI, COPII, and clathrin vesicle coats. Cell 142, 123-132
    • (2010) COPII, and Clathrin Vesicle Coats. Cell , vol.142 , pp. 123-132
    • Lee, C.1    Goldberg, J.2
  • 80
    • 79959413234 scopus 로고    scopus 로고
    • Evolution: On a bender-BARs, ESCRTs, COPs, and finally getting your coat
    • Field, M. C., Sali, A., and Rout, M. P. (2011) Evolution: on a bender-BARs, ESCRTs, COPs, and finally getting your coat. J. Cell Biol. 193, 963-972
    • (2011) J. Cell Biol. , vol.193 , pp. 963-972
    • Field, M.C.1    Sali, A.2    Rout, M.P.3
  • 83
    • 84878127508 scopus 로고    scopus 로고
    • Vesicle coats: Structure, function, and general principles of assembly
    • Faini, M., Beck, R., Wieland, F. T., and Briggs, J. A. (2013) Vesicle coats: structure, function, and general principles of assembly. Trends Cell Biol. 23, 279-288
    • (2013) Trends Cell Biol. , vol.23 , pp. 279-288
    • Faini, M.1    Beck, R.2    Wieland, F.T.3    Briggs, J.A.4
  • 86
    • 79958853077 scopus 로고    scopus 로고
    • Membrane-coating lattice scaffolds in the nuclear pore and vesicle coats: Commonalities, differences, challenges
    • Leksa, N. C., and Schwartz, T. U. (2010) Membrane-coating lattice scaffolds in the nuclear pore and vesicle coats: commonalities, differences, challenges. Nucleus 1, 314-318
    • (2010) Nucleus , vol.1 , pp. 314-318
    • Leksa, N.C.1    Schwartz, T.U.2
  • 89
    • 77951896130 scopus 로고    scopus 로고
    • Amphipathic helices and membrane curvature
    • Drin, G., and Antonny, B. (2010) Amphipathic helices and membrane curvature. FEBS Lett. 584, 1840-1847
    • (2010) FEBS Lett. , vol.584 , pp. 1840-1847
    • Drin, G.1    Antonny, B.2
  • 90
    • 0027287349 scopus 로고
    • Architecture of the Xenopus nuclear pore complex revealed by three-dimensional cryo-electron microscopy
    • Akey, C. W., and Radermacher, M. (1993) Architecture of the Xenopus nuclear pore complex revealed by three-dimensional cryo-electron microscopy. J. Cell Biol. 122, 1-19
    • (1993) J. Cell Biol. , vol.122 , pp. 1-19
    • Akey, C.W.1    Radermacher, M.2


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