4xmn

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Structure of the yeast coat nucleoporin complex, space group P212121Structure of the yeast coat nucleoporin complex, space group P212121

Structural highlights

4xmn is a 7 chain structure with sequence from Baker's yeast and Synthetic construct sequences. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Gene:SEC13, ANU3, YLR208W, L8167.4 (Baker's yeast), NUP145, RAT10, YGL092W (Baker's yeast), NUP84, YDL116W (Baker's yeast), NUP120, RAT2, YKL057C, YKL313, YKL314 (Baker's yeast), NUP85, RAT9, YJR042W, J1624 (Baker's yeast)
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[NU120_YEAST] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. NUP120 is involved in nuclear poly(A)+ RNA and pre-ribosome export, in GSP1 nuclear import, in NPC assembly and distribution, as well as in nuclear envelope organization.[1] [2] [3] [4] [5] [SEC13_YEAST] Functions as a component of the nuclear pore complex (NPC) and the COPII coat. It is one of 5 proteins constituting the COPII coat, which is involved in anterograde (ER to Golgi) double-membrane transport vesicle formation. First the small GTPase SAR1, activated by and binding to the integral ER membrane protein SEC12, exchanges GDP for GTP and recruits the heterodimer SEC23/24, which in turn recruits the heterotetramer SEC13-SEC31. The polymerization of COPII coat complexes then causes physically the deformation (budding) of the membrane, leading to the creation of a transport vesicle. The COPII complex is dissociated upon SAR1-GTP hydrolysis to SAR1-GDP. SEC23 functions as the SAR1 GTPase activating protein, whose activity is stimulated in the presence of SEC13/31. SEC13 is directly or indirectly required for normal ER membrane and nuclear envelope morphology. It also functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. SEC13 is required for efficient mRNA export from the nucleus to the cytoplasm and for correct nuclear pore biogenesis and distribution. Component of the SEA complex which coats the vacuolar membrane and is involved in intracellular trafficking, autophagy, response to nitrogen starvation, and amino acid biogenesis.[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [NUP84_YEAST] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. NUP84 is involved in nuclear poly(A)+ RNA export, in NPC assembly and distribution, as well as in nuclear envelope organization.[25] [26] [NU145_YEAST] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. Active directional transport is assured by both, a Phe-Gly (FG) repeat affinity gradient for these transport factors across the NPC and a transport cofactor concentration gradient across the nuclear envelope (GSP1 and GSP2 GTPases associated predominantly with GTP in the nucleus, with GDP in the cytoplasm). NUP145 is autocatalytically cleaved in vivo in 2 polypeptides which assume different functions in the NPC. NUP145N as one of the FG repeat nucleoporins participates in karyopherin interactions and contains part of the autocatalytic cleavage activity. NUP145C as part of the NUP84 complex is involved in nuclear poly(A)+ RNA and tRNA export. It is also required for normal NPC distribution (probably through interactions with MLP1 and MLP2) and NPC assembly, as well as for normal nuclear envelope organization.[27] [28] [29] [30] [31] [32] [33] [34] [35] [NUP85_YEAST] Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. NUP85 is involved in nuclear poly(A)+ RNA and pre-ribosome export, in GSP1 nuclear import, in NPC assembly and distribution, as well as in nuclear envelope organization.[36] [37] [38] [39] [40] [41]

Publication Abstract from PubMed

The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. Despite half a century of structural characterization, the architecture of the NPC remains unknown. Here we present the crystal structure of a reconstituted ~400-kilodalton coat nucleoporin complex (CNC) from Saccharomyces cerevisiae at a 7.4 angstrom resolution. The crystal structure revealed a curved Y-shaped architecture and the molecular details of the coat nucleoporin interactions forming the central "triskelion" of the Y. A structural comparison of the yeast CNC with an electron microscopy reconstruction of its human counterpart suggested the evolutionary conservation of the elucidated architecture. Moreover, 32 copies of the CNC crystal structure docked readily into a cryoelectron tomographic reconstruction of the fully assembled human NPC, thereby accounting for ~16 megadalton of its mass.

Nuclear pores. Architecture of the nuclear pore complex coat.,Stuwe T, Correia AR, Lin DH, Paduch M, Lu VT, Kossiakoff AA, Hoelz A Science. 2015 Mar 6;347(6226):1148-52. doi: 10.1126/science.aaa4136. Epub 2015, Feb 12. PMID:25745173[42]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Heath CV, Copeland CS, Amberg DC, Del Priore V, Snyder M, Cole CN. Nuclear pore complex clustering and nuclear accumulation of poly(A)+ RNA associated with mutation of the Saccharomyces cerevisiae RAT2/NUP120 gene. J Cell Biol. 1995 Dec;131(6 Pt 2):1677-97. PMID:8557737
  2. ↑ Siniossoglou S, Wimmer C, Rieger M, Doye V, Tekotte H, Weise C, Emig S, Segref A, Hurt EC. A novel complex of nucleoporins, which includes Sec13p and a Sec13p homolog, is essential for normal nuclear pores. Cell. 1996 Jan 26;84(2):265-75. PMID:8565072
  3. ↑ Stage-Zimmermann T, Schmidt U, Silver PA. Factors affecting nuclear export of the 60S ribosomal subunit in vivo. Mol Biol Cell. 2000 Nov;11(11):3777-89. PMID:11071906
  4. ↑ Lutzmann M, Kunze R, Buerer A, Aebi U, Hurt E. Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins. EMBO J. 2002 Feb 1;21(3):387-97. PMID:11823431 doi:10.1093/emboj/21.3.387
  5. ↑ Gao H, Sumanaweera N, Bailer SM, Stochaj U. Nuclear accumulation of the small GTPase Gsp1p depends on nucleoporins Nup133p, Rat2p/Nup120p, Nup85p, Nic96p, and the acetyl-CoA carboxylase Acc1p. J Biol Chem. 2003 Jul 11;278(28):25331-40. Epub 2003 May 1. PMID:12730220 doi:http://dx.doi.org/10.1074/jbc.M301607200
  6. ↑ Siniossoglou S, Wimmer C, Rieger M, Doye V, Tekotte H, Weise C, Emig S, Segref A, Hurt EC. A novel complex of nucleoporins, which includes Sec13p and a Sec13p homolog, is essential for normal nuclear pores. Cell. 1996 Jan 26;84(2):265-75. PMID:8565072
  7. ↑ Novick P, Field C, Schekman R. Identification of 23 complementation groups required for post-translational events in the yeast secretory pathway. Cell. 1980 Aug;21(1):205-15. PMID:6996832
  8. ↑ Novick P, Ferro S, Schekman R. Order of events in the yeast secretory pathway. Cell. 1981 Aug;25(2):461-9. PMID:7026045
  9. ↑ Kaiser CA, Schekman R. Distinct sets of SEC genes govern transport vesicle formation and fusion early in the secretory pathway. Cell. 1990 May 18;61(4):723-33. PMID:2188733
  10. ↑ Bednarek SY, Ravazzola M, Hosobuchi M, Amherdt M, Perrelet A, Schekman R, Orci L. COPI- and COPII-coated vesicles bud directly from the endoplasmic reticulum in yeast. Cell. 1995 Dec 29;83(7):1183-96. PMID:8548805
  11. ↑ Kuehn MJ, Schekman R, Ljungdahl PO. Amino acid permeases require COPII components and the ER resident membrane protein Shr3p for packaging into transport vesicles in vitro. J Cell Biol. 1996 Nov;135(3):585-95. PMID:8909535
  12. ↑ Roberg KJ, Bickel S, Rowley N, Kaiser CA. Control of amino acid permease sorting in the late secretory pathway of Saccharomyces cerevisiae by SEC13, LST4, LST7 and LST8. Genetics. 1997 Dec;147(4):1569-84. PMID:9409822
  13. ↑ Roberg KJ, Rowley N, Kaiser CA. Physiological regulation of membrane protein sorting late in the secretory pathway of Saccharomyces cerevisiae. J Cell Biol. 1997 Jun 30;137(7):1469-82. PMID:9199164
  14. ↑ Sutterlin C, Doering TL, Schimmoller F, Schroder S, Riezman H. Specific requirements for the ER to Golgi transport of GPI-anchored proteins in yeast. J Cell Sci. 1997 Nov;110 ( Pt 21):2703-14. PMID:9427388
  15. ↑ Campbell JL, Schekman R. Selective packaging of cargo molecules into endoplasmic reticulum-derived COPII vesicles. Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):837-42. PMID:9023343
  16. ↑ Matsuoka K, Schekman R. The use of liposomes to study COPII- and COPI-coated vesicle formation and membrane protein sorting. Methods. 2000 Apr;20(4):417-28. PMID:10720463 doi:10.1006/meth.2000.0955
  17. ↑ Siniossoglou S, Lutzmann M, Santos-Rosa H, Leonard K, Mueller S, Aebi U, Hurt E. Structure and assembly of the Nup84p complex. J Cell Biol. 2000 Apr 3;149(1):41-54. PMID:10747086
  18. ↑ Lederkremer GZ, Cheng Y, Petre BM, Vogan E, Springer S, Schekman R, Walz T, Kirchhausen T. Structure of the Sec23p/24p and Sec13p/31p complexes of COPII. Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10704-9. Epub 2001 Sep 4. PMID:11535824 doi:10.1073/pnas.191359398
  19. ↑ Matsuoka K, Schekman R, Orci L, Heuser JE. Surface structure of the COPII-coated vesicle. Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13705-9. PMID:11717432 doi:10.1073/pnas.241522198
  20. ↑ Ryan KJ, Wente SR. Isolation and characterization of new Saccharomyces cerevisiae mutants perturbed in nuclear pore complex assembly. BMC Genet. 2002 Sep 5;3:17. Epub 2002 Sep 5. PMID:12215173
  21. ↑ Lutzmann M, Kunze R, Buerer A, Aebi U, Hurt E. Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins. EMBO J. 2002 Feb 1;21(3):387-97. PMID:11823431 doi:10.1093/emboj/21.3.387
  22. ↑ Fatal N, Suntio T, Makarow M. Selective protein exit from yeast endoplasmic reticulum in absence of functional COPII coat component Sec13p. Mol Biol Cell. 2002 Dec;13(12):4130-40. PMID:12475940 doi:10.1091/mbc.02-05-0082
  23. ↑ Sato K, Nakano A. Reconstitution of coat protein complex II (COPII) vesicle formation from cargo-reconstituted proteoliposomes reveals the potential role of GTP hydrolysis by Sar1p in protein sorting. J Biol Chem. 2004 Jan 9;279(2):1330-5. Epub 2003 Nov 19. PMID:14627716 doi:10.1074/jbc.C300457200
  24. ↑ Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, Williams R, Salamero J, Chait BT, Sali A, Field MC, Rout MP, Dargemont C. A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics. 2011 Jun;10(6):M110.006478. doi: 10.1074/mcp.M110.006478., Epub 2011 Mar 31. PMID:21454883 doi:10.1074/mcp.M110.006478
  25. ↑ Siniossoglou S, Wimmer C, Rieger M, Doye V, Tekotte H, Weise C, Emig S, Segref A, Hurt EC. A novel complex of nucleoporins, which includes Sec13p and a Sec13p homolog, is essential for normal nuclear pores. Cell. 1996 Jan 26;84(2):265-75. PMID:8565072
  26. ↑ Lutzmann M, Kunze R, Buerer A, Aebi U, Hurt E. Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins. EMBO J. 2002 Feb 1;21(3):387-97. PMID:11823431 doi:10.1093/emboj/21.3.387
  27. ↑ Fabre E, Boelens WC, Wimmer C, Mattaj IW, Hurt EC. Nup145p is required for nuclear export of mRNA and binds homopolymeric RNA in vitro via a novel conserved motif. Cell. 1994 Jul 29;78(2):275-89. PMID:8044840
  28. ↑ Wente SR, Blobel G. NUP145 encodes a novel yeast glycine-leucine-phenylalanine-glycine (GLFG) nucleoporin required for nuclear envelope structure. J Cell Biol. 1994 Jun;125(5):955-69. PMID:8195299
  29. ↑ Sharma K, Fabre E, Tekotte H, Hurt EC, Tollervey D. Yeast nucleoporin mutants are defective in pre-tRNA splicing. Mol Cell Biol. 1996 Jan;16(1):294-301. PMID:8524308
  30. ↑ Teixeira MT, Siniossoglou S, Podtelejnikov S, Benichou JC, Mann M, Dujon B, Hurt E, Fabre E. Two functionally distinct domains generated by in vivo cleavage of Nup145p: a novel biogenesis pathway for nucleoporins. EMBO J. 1997 Aug 15;16(16):5086-97. PMID:9305650 doi:10.1093/emboj/16.16.5086
  31. ↑ Teixeira MT, Fabre E, Dujon B. Self-catalyzed cleavage of the yeast nucleoporin Nup145p precursor. J Biol Chem. 1999 Nov 5;274(45):32439-44. PMID:10542288
  32. ↑ Galy V, Olivo-Marin JC, Scherthan H, Doye V, Rascalou N, Nehrbass U. Nuclear pore complexes in the organization of silent telomeric chromatin. Nature. 2000 Jan 6;403(6765):108-12. PMID:10638763 doi:10.1038/47528
  33. ↑ Lutzmann M, Kunze R, Buerer A, Aebi U, Hurt E. Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins. EMBO J. 2002 Feb 1;21(3):387-97. PMID:11823431 doi:10.1093/emboj/21.3.387
  34. ↑ Denning DP, Patel SS, Uversky V, Fink AL, Rexach M. Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded. Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2450-5. Epub 2003 Feb 25. PMID:12604785 doi:10.1073/pnas.0437902100
  35. ↑ Strawn LA, Shen T, Shulga N, Goldfarb DS, Wente SR. Minimal nuclear pore complexes define FG repeat domains essential for transport. Nat Cell Biol. 2004 Mar;6(3):197-206. Epub 2004 Feb 22. PMID:15039779 doi:10.1038/ncb1097
  36. ↑ Goldstein AL, Snay CA, Heath CV, Cole CN. Pleiotropic nuclear defects associated with a conditional allele of the novel nucleoporin Rat9p/Nup85p. Mol Biol Cell. 1996 Jun;7(6):917-34. PMID:8816998
  37. ↑ Santos-Rosa H, Moreno H, Simos G, Segref A, Fahrenkrog B, Pante N, Hurt E. Nuclear mRNA export requires complex formation between Mex67p and Mtr2p at the nuclear pores. Mol Cell Biol. 1998 Nov;18(11):6826-38. PMID:9774696
  38. ↑ Stage-Zimmermann T, Schmidt U, Silver PA. Factors affecting nuclear export of the 60S ribosomal subunit in vivo. Mol Biol Cell. 2000 Nov;11(11):3777-89. PMID:11071906
  39. ↑ Allen NP, Patel SS, Huang L, Chalkley RJ, Burlingame A, Lutzmann M, Hurt EC, Rexach M. Deciphering networks of protein interactions at the nuclear pore complex. Mol Cell Proteomics. 2002 Dec;1(12):930-46. PMID:12543930
  40. ↑ Lutzmann M, Kunze R, Buerer A, Aebi U, Hurt E. Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins. EMBO J. 2002 Feb 1;21(3):387-97. PMID:11823431 doi:10.1093/emboj/21.3.387
  41. ↑ Gao H, Sumanaweera N, Bailer SM, Stochaj U. Nuclear accumulation of the small GTPase Gsp1p depends on nucleoporins Nup133p, Rat2p/Nup120p, Nup85p, Nic96p, and the acetyl-CoA carboxylase Acc1p. J Biol Chem. 2003 Jul 11;278(28):25331-40. Epub 2003 May 1. PMID:12730220 doi:http://dx.doi.org/10.1074/jbc.M301607200
  42. ↑ Stuwe T, Correia AR, Lin DH, Paduch M, Lu VT, Kossiakoff AA, Hoelz A. Nuclear pores. Architecture of the nuclear pore complex coat. Science. 2015 Mar 6;347(6226):1148-52. doi: 10.1126/science.aaa4136. Epub 2015, Feb 12. PMID:25745173 doi:http://dx.doi.org/10.1126/science.aaa4136

4xmn, resolution 7.60Å

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