Crystal structure of human nuclear pore complex component NUP43

FEBS Letters

Volumn 589, Issue 21, 2015, Pages 3247-3253

  Xu, Chao ^a,b   Li, Zhihong ^a   He, Hao ^a   Wernimont, Amy ^a   Li, Yanjun ^a   Loppnau, Peter ^a   Min, Jinrong ^a,c  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

Nup107 subcomplex; Nup43; Nup85; Seh1L; WD40 repeat

Indexed keywords

ARGININE; ASPARTIC ACID; GLUTAMINE; GLYCINE; LYSINE; METHIONINE; NUCLEOPORIN; NUCLEOPORIN NUP107; NUCLEOPORIN NUP133; NUCLEOPORIN NUP43; NUCLEOPORIN NUP85; PHENYLALANINE; PROTEIN SEH1L; SERINE; THREONINE; UNCLASSIFIED DRUG; NUP133 PROTEIN, HUMAN; NUP43 PROTEIN, HUMAN; NUP85 PROTEIN, HUMAN;

AMINO ACID SEQUENCE; ANIMAL CELL; ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; ESCHERICHIA COLI; GEL FILTRATION; HUMAN; HYDROGEN BOND; ISOTHERMAL TITRATION CALORIMETRY; LIGAND BINDING; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PROCEDURES; PROTEIN QUATERNARY STRUCTURE; PROTEIN SECONDARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; HUMANS; MODELS, MOLECULAR; NUCLEAR PORE COMPLEX PROTEINS; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY;

EID: 84944883752     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2015.09.008     Document Type: Article

References (44)

1. C. Strambio-De-Castillia, M. Niepel, and M.P. Rout The nuclear pore complex: bridging nuclear transport and gene regulation Nat. Rev. Mol. Cell Biol. 11 2010 490 501
2. A. Cook, F. Bono, M. Jinek, and E. Conti Structural biology of nucleocytoplasmic transport Annu. Rev. Biochem. 76 2007 647 671
3. J.M. Cronshaw, A.N. Krutchinsky, W. Zhang, B.T. Chait, and M.J. Matunis Proteomic analysis of the mammalian nuclear pore complex J. Cell Biol. 158 2002 915 927
4. T.U. Schwartz Modularity within the architecture of the nuclear pore complex Curr. Opin. Struct. Biol. 15 2005 221 226
5. R.Y. Lim, and B. Fahrenkrog The nuclear pore complex up close Curr. Opin. Cell Biol. 18 2006 342 347
6. T.C. Walther, A. Alves, H. Pickersgill, I. Loiodice, M. Hetzer, V. Galy, B.B. Hulsmann, T. Kocher, M. Wilm, T. Allen, I.W. Mattaj, and V. Doye The conserved Nup107-160 complex is critical for nuclear pore complex assembly Cell 113 2003 195 206
7. C. Gonzalez-Aguilera, and P. Askjaer Dissecting the NUP107 complex: multiple components and even more functions Nucleus 3 2012 340 348
8. I. Loiodice, A. Alves, G. Rabut, M. Van Overbeek, J. Ellenberg, J.B. Sibarita, and V. Doye The entire Nup107-160 complex, including three new members, is targeted as one entity to kinetochores in mitosis Mol. Biol. Cell 15 2004 3333 3344
9. T. Stuwe, A.R. Correia, D.H. Lin, M. Paduch, V.T. Lu, A.A. Kossiakoff, and A. Hoelz Nuclear pores. Architecture of the nuclear pore complex coat Science 347 2015 1148 1152
10. I.C. Berke, T. Boehmer, G. Blobel, and T.U. Schwartz Structural and functional analysis of Nup133 domains reveals modular building blocks of the nuclear pore complex J. Cell Biol. 167 2004 591 597
11. T. Boehmer, S. Jeudy, I.C. Berke, and T.U. Schwartz Structural and functional studies of Nup107/Nup133 interaction and its implications for the architecture of the nuclear pore complex Mol. Cell 30 2008 721 731
12. S.G. Brohawn, N.C. Leksa, E.D. Spear, K.R. Rajashankar, and T.U. Schwartz Structural evidence for common ancestry of the nuclear pore complex and vesicle coats Science 322 2008 1369 1373
13. E.W. Debler, Y. Ma, H.S. Seo, K.C. Hsia, T.R. Noriega, G. Blobel, and A. Hoelz A fence-like coat for the nuclear pore membrane Mol. Cell 32 2008 815 826
14. K.C. Hsia, P. Stavropoulos, G. Blobel, and A. Hoelz Architecture of a coat for the nuclear pore membrane Cell 131 2007 1313 1326
15. S.G. Brohawn, and T.U. Schwartz Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice Nat. Struct. Mol. Biol. 16 2009 1173 1177
16. V. Nagy, K.C. Hsia, E.W. Debler, M. Kampmann, A.M. Davenport, G. Blobel, and A. Hoelz Structure of a trimeric nucleoporin complex reveals alternate oligomerization states Proc. Natl. Acad. Sci. USA 106 2009 17693 17698
17. H.S. Seo, Y. Ma, E.W. Debler, D. Wacker, S. Kutik, G. Blobel, and A. Hoelz Structural and functional analysis of Nup120 suggests ring formation of the Nup84 complex Proc. Natl. Acad. Sci. USA 106 2009 14281 14286
18. N.C. Leksa, S.G. Brohawn, and T.U. Schwartz The structure of the scaffold nucleoporin Nup120 reveals a new and unexpected domain architecture Structure 17 2009 1082 1091
19. X. Liu, J.M. Mitchell, R.W. Wozniak, G. Blobel, and J. Fan Structural evolution of the membrane-coating module of the nuclear pore complex Proc. Natl. Acad. Sci. USA 109 2012 16498 16503
20. K. Kelley, K.E. Knockenhauer, G. Kabachinski, and T.U. Schwartz Atomic structure of the Y complex of the nuclear pore Nat. Struct. Mol. Biol. 22 2015 425 431
21. K.H. Bui, A. von Appen, A.L. DiGuilio, A. Ori, L. Sparks, M.T. Mackmull, T. Bock, W. Hagen, A. Andres-Pons, J.S. Glavy, and M. Beck Integrated structural analysis of the human nuclear pore complex scaffold Cell 155 2013 1233 1243
22. K. Thierbach, A. von Appen, M. Thoms, M. Beck, D. Flemming, and E. Hurt Protein interfaces of the conserved Nup84 complex from Chaetomium thermophilum shown by crosslinking mass spectrometry and electron microscopy Structure 21 2013 1672 1682
23. M. Lutzmann, R. Kunze, A. Buerer, U. Aebi, and E. Hurt Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins EMBO J. 21 2002 387 397
24. C. Xu, and J. Min Structure and function of WD40 domain proteins Protein Cell 2 2011 202 214
25. C. Xu, C. Bian, W. Yang, M. Galka, H. Ouyang, C. Chen, W. Qiu, H. Liu, A.E. Jones, F. MacKenzie, P. Pan, S.S. Li, H. Wang, and J. Min Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2) Proc. Natl. Acad. Sci. USA 107 2010 19266 19271
26. A. Schuetz, A. Allali-Hassani, F. Martin, P. Loppnau, M. Vedadi, A. Bochkarev, A.N. Plotnikov, C.H. Arrowsmith, and J. Min Structural basis for molecular recognition and presentation of histone H3 by WDR5 EMBO J. 25 2006 4245 4252
27. N. Neumann, D. Lundin, and A.M. Poole Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor PLoS One 5 2010 e13241
28. X.H. Wu, Y. Wang, Z. Zhuo, F. Jiang, and Y.D. Wu Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by beta-bulges and DHSW tetrads PLoS One 7 2012 e43005
29. P. Grochulski, M.N. Fodje, J. Gorin, S.L. Labiuk, and R. Berg Beamline 08ID-1, the prime beamline of the Canadian macromolecular crystallography facility J. Synchrotron Radiat. 18 2011 681 684
30. W. Kabsch XDS Acta Crystallogr. D Biol. Crystallogr. 66 2010 125 132
31. P.R. Evans An introduction to data reduction: space-group determination, scaling and intensity statistics Acta Crystallogr. D Biol. Crystallogr. 67 2011 282 292
32. A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni, and R.J. Read Phaser crystallographic software J. Appl. Crystallogr. 40 2007 658 674
33. L. Jaroszewski, L. Rychlewski, Z. Li, W. Li, and A. Godzik FFAS03: a server for profile-profile sequence alignments Nucleic Acids Res. 33 2005 W284 W288
34. A.A. Canutescu, A.A. Shelenkov, and R.L. Dunbrack Jr. A graph-theory algorithm for rapid protein side-chain prediction Protein Sci. 12 2003 2001 2014
35. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne The protein data bank Nucleic Acids Res. 28 2000 235 242
36. J. Rabl, M. Leibundgut, S.F. Ataide, A. Haag, and N. Ban Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1 Science 331 2011 730 736
37. N.V. Murzina, X.Y. Pei, W. Zhang, M. Sparkes, J. Vicente-Garcia, J.V. Pratap, S.H. McLaughlin, T.R. Ben-Shahar, A. Verreault, B.F. Luisi, and E.D. Laue Structural basis for the recognition of histone H4 by the histone-chaperone RbAp46 Structure 16 2008 1077 1085
38. D. Ruiz Carrillo, R. Chandrasekaran, M. Nilsson, T. Cornvik, C.W. Liew, S.M. Tan, and J. Lescar Structure of human Rack1 protein at a resolution of 2.45 A Acta Crystallogr. Sect. F: Struct. Biol. Cryst. Commun. 68 2012 867 872
39. A. Perrakis, T.K. Sixma, K.S. Wilson, and V.S. Lamzin WARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models Acta Crystallogr. D Biol. Crystallogr. 53 1997 448 455
40. G. Langer, S.X. Cohen, V.S. Lamzin, and A. Perrakis Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 Nat. Protoc. 3 2008 1171 1179
41. P. Emsley, B. Lohkamp, W.G. Scott, and K. Cowtan Features and development of coot Acta Crystallogr. D Biol. Crystallogr. 66 2010 486 501
42. G.N. Murshudov, P. Skubak, A.A. Lebedev, N.S. Pannu, R.A. Steiner, R.A. Nicholls, M.D. Winn, F. Long, and A.A. Vagin REFMAC5 for the refinement of macromolecular crystal structures Acta Crystallogr. D Biol. Crystallogr. 67 2011 355 367
43. V.B. Chen, W.B. Arendall 3rd, J.J. Headd, D.A. Keedy, R.M. Immormino, G.J. Kapral, L.W. Murray, J.S. Richardson, and D.C. Richardson MolProbity: all-atom structure validation for macromolecular crystallography Acta Crystallogr. D Biol. Crystallogr. 66 2010 12 21
44. C. Xu, C. Bian, R. Lam, A. Dong, and J. Min The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain Nat. Commun. 2 2011 227