Crystal structure of the nipah virus phosphoprotein tetramerization domain

Journal of Virology

Volumn 88, Issue 1, 2014, Pages 758-762

  Bruhn, Jessica F ^a   Barnett, Katherine C ^a,d   Bibby, Jaclyn ^b   Thomas, Jens M H ^b   Keegan, Ronan M ^c   Rigden, Daniel J ^b   Bornholdt, Zachary A ^a   Saphire, Erica Ollmann ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF LIVERPOOL   (United Kingdom)

^c RUTHERFORD APPLETON LABORATORY   (United Kingdom)

^d HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS PHOSPHOPROTEIN;

ALPHA HELIX; ARTICLE; CRYSTAL STRUCTURE; NIPAH VIRUS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE; RNA SEQUENCE; RNA STRUCTURE;

BIOPOLYMERS; CRYSTALLOGRAPHY, X-RAY; NIPAH VIRUS; PHOSPHOPROTEINS; PROTEIN CONFORMATION;

EID: 84890866364     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.02294-13     Document Type: Article

References (49)

1. Lee B, Rota PA. 2012. Henipavirus: ecology, molecular virology, and pathogenesis. Springer, Heidelberg, Germany.
2. Rockx B, Wang LF. 2013. Zoonotic henipavirus transmission. J. Clin. Virol. 58:354-356. http://dx.doi.org/10.1016/j.jcv.2013.02.013.
3. Broder CC. 2012. Henipavirus outbreaks to antivirals: the current status of potential therapeutics. Curr. Opin. Virol. 2:176-187. http://dx.doi.org /10.1016/j.coviro.2012.02.016.
4. Morin B, Kranzusch PJ, Rahmeh AA, Whelan SP. 2013. The polymerase of negative-stranded RNA viruses. Curr. Opin. Virol. 3:103-110. http://dx .doi.org/10.1016/j.coviro.2013.03.008.
5. Habchi J, Longhi S. 2012. Structural disorder within paramyxovirus nucleoproteins and phosphoproteins. Mol. Biosyst. 8:69-81. http://dx .doi.org/10.1039/c1mb05204g.
6. Basler CF. 2012. Nipah and hendra virus interactions with the innate immune system. Curr. Top. Microbiol. Immunol. 359:123-152. http://dx .doi.org/10.1007/82_2012_209.
7. Lo MK, Peeples ME, Bellini WJ, Nichol ST, Rota PA, Spiropoulou CF. 2012. Distinct and overlapping roles of Nipah virus P gene products in modulating the human endothelial cell antiviral response. PLoS One 7:e47790. http://dx.doi.org/10.1371/journal.pone.0047790.
8. Chan YP, Koh CL, Lam SK, Wang LF. 2004. Mapping of domains responsible for nucleocapsid protein-phosphoprotein interaction of henipaviruses. J. Gen. Virol. 85:1675-1684. http://dx.doi.org/10.1099/vir.0.19752-0.
9. Habchi J, Blangy S, Mamelli L, Jensen MR, Blackledge M, Darbon H, Oglesbee M, Shu Y, Longhi S. 2011. Characterization of the interactions between the nucleoprotein and the phosphoprotein of Henipavirus. J. Biol. Chem. 286:13583-13602. http://dx.doi.org/10.1074/jbc.M111.219857.
10. Omi-Furutani M, Yoneda M, Fujita K, Ikeda F, Kai C. 2010. Novel phosphoprotein-interacting region in Nipah virus nucleocapsid protein and its involvement in viral replication. J. Virol. 84:9793-9799. http://dx .doi.org/10.1128/JVI.00339-10.
11. Chen M, Ogino T, Banerjee AK. 2006. Mapping and functional role of the self-association domain of vesicular stomatitis virus phosphoprotein. J. Virol. 80:9511-9518. http://dx.doi.org/10.1128/JVI.01035-06.
12. Schneider U, Blechschmidt K, Schwemmle M, Staeheli P. 2004. Overlap of interaction domains indicates a central role of the P protein in assembly and regulation of the Borna disease virus polymerase complex. J. Biol. Chem. 279:55290-55296. http://dx.doi.org/10.1074/jbc.M408913200.
13. Communie G, Crepin T, Maurin D, Jensen MR, Blackledge M, Ruigrok RW. 2013. Structure of the tetramerization domain of measles virus phosphoprotein. J. Virol. 87:7166-7169. http://dx.doi.org/10.1128/JVI.00487-13.
14. Cox R, Green TJ, Purushotham S, Deivanayagam C, Bedwell GJ, Prevelige PE, Luo M. 2013. Structural and functional characterization of the mumps virus phosphoprotein. J. Virol. 87:7558-7568. http://dx.doi.org /10.1128/JVI.00653-13.
15. Tarbouriech N, Curran J, Ruigrok RW, Burmeister WP. 2000. Tetrameric coiled coil domain of Sendai virus phosphoprotein. Nat. Struct. Biol. 7:777-781. http://dx.doi.org/10.1038/79013.
16. Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R. 2010. A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res. 38:W695-699. http://dx.doi.org/10.1093/nar/gkq313.
17. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, Mc-William H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948. http://dx.doi.org/10.1093/bioinformatics/btm404.
18. Blocquel D, Beltrandi M, Erales J, Barbier P, Longhi S. 2013. Biochemical and structural studies of the oligomerization domain of the Nipah virus phosphoprotein: evidence for an elongated coiled-coil homotrimer. Virology 466:162-172. http://dx.doi.org/10.1016/j.virol.2013.07.031.
19. Otwinowski Z, Minor W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:307-326. http://dx .doi.org/10.1016/S0076-6879(97)76066-X.
20. Pflugrath JW. 1999. The finer things in X-ray diffraction data collection. Acta Crystallogr. D Biol. Crystallogr. 55:1718-1725. http://dx.doi.org/10 .1107/S090744499900935X.
21. Reference deleted.
22. Read RJ, James MNG. 1988. Refined crystal structure of Streptomyces griseus trypsin at 1.7 A resolution. J. Mol. Biol. 200:523-551. http://dx.doi .org/10.1016/0022-2836(88)90541-4.
23. Read RJ, Schierbeek AJ. 1988. A phased translation function. J. Appl. Crystallogr. 21:490-495. http://dx.doi.org/10.1107/S002188988800562X.
24. Caliandro R, Dibenedetto D, Cascarano GL, Mazzone A, Nico G. 2012. Automatic alpha-helix identification in Patterson maps. Acta Crystallogr.DBiol. Crystallogr. 68:1-12. http://dx.doi.org/10.1107/S0108767311041353.
25. Tu D, Li Y, Song HK, Toms AV, Gould CJ, Ficarro SB, Marto JA, Goode BL, Eck MJ. 2011. Crystal structure of a coiled-coil domain from human ROCK I. PLoS One 6:e18080. http://dx.doi.org/10.1371/journal .pone.0018080.
26. Bibby J, Keegan RM, Mayans O, Winn MD, Rigden DJ. 2012. AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models. Acta Crystallogr. D Biol. Crystallogr. 68:1622-1631. http://dx.doi.org/10.1107 /S0907444912039194.
27. Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. 2006. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc. Natl. Acad. Sci. U. S. A. 103:5361-5366.
28. Vagin A, Teplyakov A. 2010. Molecular replacement with MOLREP. Acta Crystallogr. D Biol. Crystallogr. 66:22-25. http://dx.doi.org/10.1107 /S0108767309045206.
29. Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. 2011. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr.DBiol. Crystallogr. 67:355-367. http://dx.doi.org/10.1107/S0907444911001314.
30. Sheldrick GM. 2008. A short history of SHELX. Acta Crystallogr. A 64: 112-122. http://dx.doi.org/10.1107/S0108767307043930.
31. Langer G, Cohen SX, Lamzin VS, Perrakis A. 2008. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protoc. 3:1171-1179. http://dx.doi.org/10.1038/nprot .2008.91.
32. Cowtan K. 2006. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. D Biol. Crystallogr. 62:1002-1011. http://dx.doi.org/10.1107/S0907444906022116.
33. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. 2010. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr.DBiol. Crystallogr. 66:213-221. http://dx.doi .org/10.1107/S0907444909052925.
34. Emsley P, Lohkamp B, Scott WG, Cowtan K. 2010. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66:486-501. http: //dx.doi.org/10.1107/S0907444910007493.
35. Grigoryan G, Degrado WF. 2011. Probing designability via a generalized model of helical bundle geometry. J. Mol. Biol. 405:1079-1100. http://dx .doi.org/10.1016/j.jmb.2010.08.058.
36. Walshaw J, Woolfson DN. 2001. Socket: a program for identifying and analysing coiled-coil motifs within protein structures. J. Mol. Biol. 307: 1427-1450. http://dx.doi.org/10.1006/jmbi.2001.4545.
37. Krissinel E, Henrick K. 2007. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372:774-797. http://dx.doi.org/10 .1016/j.jmb.2007.05.022.
38. Ramos J, Lazaridis T. 2011. Computational analysis of residue contributions to coiled-coil topology. Protein Sci. 20:1845-1855. http://dx.doi.org /10.1002/pro.718.
39. Bowman MC, Smallwood S, Moyer SA. 1999. Dissection of individual functions of the Sendai virus phosphoprotein in transcription. J. Virol. 73:6474-6483.
40. Ding H, Green TJ, Lu S, Luo M. 2006. Crystal structure of the oligomerization domain of the phosphoprotein of vesicular stomatitis virus. J. Virol. 80:2808-2814. http://dx.doi.org/10.1128/JVI.80.6.2808-2814.2006.
41. Ivanov I, Crepin T, Jamin M, Ruigrok RW. 2010. Structure of the dimerization domain of the rabies virus phosphoprotein. J. Virol. 84: 3707-3710. http://dx.doi.org/10.1128/JVI.02557-09.
42. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. 2001. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. U. S. A. 98:10037-10041. http://dx.doi.org/10.1073 /pnas.181342398.
43. Takacs AM, Banerjee AK. 1995. Efficient interaction of the vesicular stomatitis virus P protein with the L protein or the N protein in cells expressing the recombinant proteins. Virology 208:821-826. http://dx .doi.org/10.1006/viro.1995.1219.
44. Tan WS, Ong ST, Eshaghi M, Foo SS, Yusoff K. 2004. Solubility, immunogenicity and physical properties of the nucleocapsid protein of Nipah virus produced in Escherichia coli. J. Med. Virol. 73:105-112. http: //dx.doi.org/10.1002/jmv.20052.
45. Rahmeh AA, Schenk AD, Danek EI, Kranzusch PJ, Liang B, Walz T, Whelan SP. 2010. Molecular architecture of the vesicular stomatitis virus RNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 107:20075-20080. http: //dx.doi.org/10.1073/pnas.1013559107.
46. Kingston RL, Hamel DJ, Gay LS, Dahlquist FW, Matthews BW. 2004. Structural basis for the attachment of a paramyxoviral polymerase to its template. Proc. Natl. Acad. Sci. U. S. A. 101:8301-8306. http://dx.doi.org /10.1073/pnas.0402690101.
47. Egelman EH, Wu SS, Amrein M, Portner A, Murti G. 1989. The Sendai virus nucleocapsid exists in at least four different helical states. J. Virol. 63:2233-2243.
48. Gao Y, Lenard J. 1995. Cooperative binding of multimeric phosphoprotein (P) of vesicular stomatitis virus to polymerase (L) and template: pathways of assembly. J. Virol. 69:7718-7723.
49. Gao Y, Lenard J. 1995. Multimerization and transcriptional activation of the phosphoprotein (P) of vesicular stomatitis virus by casein kinase-II. EMBO J. 14:1240-1247.