Structure of a Murine Norovirus NS6 Protease-Product Complex Revealed by Adventitious Crystallisation
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{"title"=>"Structure of a murine norovirus NS6 protease-product complex revealed by adventitious crystallisation", "type"=>"journal", "authors"=>[{"first_name"=>"Eoin N.", "last_name"=>"Leen", "scopus_author_id"=>"55246787200"}, {"first_name"=>"Gabriela", "last_name"=>"Baeza", "scopus_author_id"=>"56330090700"}, {"first_name"=>"Stephen", "last_name"=>"Curry", "scopus_author_id"=>"7203018468"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84862001870", "sgr"=>"84862001870", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0038723", "pmid"=>"22685603", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pui"=>"364979314"}, "id"=>"245baf75-4171-3d33-ad85-5c834d3f8586", "abstract"=>"Murine noroviruses have emerged as a valuable tool for investigating the molecular basis of infection and pathogenesis of the closely related human noroviruses, which are the major cause of non-bacterial gastroenteritis. The replication of noroviruses relies on the proteolytic processing of a large polyprotein precursor into six non-structural proteins (NS1-2, NS3, NS4, NS5, NS6(pro), NS7(pol)) by the virally-encoded NS6 protease. We report here the crystal structure of MNV NS6(pro), which has been determined to a resolution of 1.6 Å. Adventitiously, the crystal contacts are mediated in part by the binding of the C-terminus of NS6(pro) within the peptide-binding cleft of a neighbouring molecule. This insertion occurs for both molecules in the asymmetric unit of the crystal in a manner that is consistent with physiologically-relevant binding, thereby providing two independent views of a protease-peptide complex. Since the NS6(pro) C-terminus is formed in vivo by NS6(pro) processing, these crystal contacts replicate the protease-product complex that is formed immediately following cleavage of the peptide bond at the NS6-NS7 junction. The observed mode of binding of the C-terminal product peptide yields new insights into the structural basis of NS6(pro) specificity.", "link"=>"http://www.mendeley.com/research/structure-murine-norovirus-ns6-proteaseproduct-complex-revealed-adventitious-crystallisation", "reader_count"=>23, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>1, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>1, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Medicine and Dentistry"=>3, "Agricultural and Biological Sciences"=>15, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United Kingdom"=>1, "Germany"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/626859"], "description"=>"1<p>Values for highest resolution shell given in parentheses.</p>2<p>R<sub>merge</sub>  = 100 ×Σ<sub>hkl</sub>|I<sub>j</sub>(hkl) − j(hkl)>|/Σ<sub>hkl</sub>Σ<sub>j</sub>I(hkl), where I<sub>j</sub>(hkl) and j(hkl)> are the intensity of measurement j and the mean intensity for the reflection with indices hkl, respectively.</p>3<p>R<sub>work</sub>  = 100 ×Σ<sub>hkl</sub>||F<sub>obs</sub>| − |F<sub>calc</sub>||/Σ<sub>hkl</sub>|F<sub>obs</sub>|.</p>4<p>R<sub>free</sub> is the R<sub>model</sub> calculated using a randomly selected 5% sample of reflection data that were omitted from the refinement.</p>5<p>RMS, root-mean-square; deviations are from the ideal geometry defined by the Engh and Huber parameters <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038723#pone.0038723-Engh1\" target=\"_blank\">[45]</a>.</p>", "links"=>[], "tags"=>["refinement", "mnv"], "article_id"=>297352, "categories"=>["Virology", "Biochemistry", "Infectious Diseases"], "users"=>["Eoin N. Leen", "Gabriela Baeza", "Stephen Curry"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0038723.t001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Crystallographic_data_collection_and_model_refinement_statistics_for_MNV_NS6_pro_/297352", "title"=>"Crystallographic data collection and model refinement statistics for MNV NS6<sup>pro</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 04:09:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/626824"], "description"=>"<p>Restriction sites used in cloning are underlined. Mutations introduced using QuikChange mutagenesis are in boldface.</p>", "links"=>[], "tags"=>["c139a", "mutagenic", "primers"], "article_id"=>297315, "categories"=>["Virology", "Biochemistry", "Infectious Diseases"], "users"=>["Eoin N. Leen", "Gabriela Baeza", "Stephen Curry"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0038723.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cloning_and_C139A_mutagenic_primers_used_in_the_course_of_the_study_/297315", "title"=>"Cloning and C139A mutagenic primers used in the course of the study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 04:09:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/626767"], "description"=>"<p>(A) The five cleavage junctions of MNV CW1 polyprotein (NCBI accession number YP_720001) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038723#pone.0038723-Sosnovtsev1\" target=\"_blank\">[14]</a>. (B) Weblogo of polyprotein cleavage junctions cleaved by MNV NS6<sup>pro</sup>. This Weblogo was generated using 39 MNV polyprotein sequences and the Weblogo sequence logo generator <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038723#pone.0038723-Crooks1\" target=\"_blank\">[44]</a>. The height of the letter in each case is indicative of the degree of conservation. The Genbank accession numbers of the other sequences used to prepare the alignment are ABU55618, ABU55627, ABU55615, ABU55621, ABU55612, ABU55624, AEE10026, ABU55600, AEY83582, AEE10023, ABU55606, AEE10020, ABU55609, AEE10017, ABB02416, AEE10002, ACJ72215, AEE09999, ABU55591, AEE10005, ABU55570, AEE10008, ABU55585, AEE10014, ABU55579, AEE10011, ABU55576, ABU55597, ABU55573, ABU55603, ABU55582, ABU55594, ABU55588, ABU55567, ACS70958, ACJ72218, ABS29272, ABS29274.</p>", "links"=>[], "tags"=>["polyprotein", "junction", "mnv", "cleaved"], "article_id"=>297264, "categories"=>["Virology", "Biochemistry", "Infectious Diseases"], "users"=>["Eoin N. Leen", "Gabriela Baeza", "Stephen Curry"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0038723.g004", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_conservation_of_polyprotein_junction_in_MNV_that_are_cleaved_by_NS6_pro_/297264", "title"=>"Sequence conservation of polyprotein junction in MNV that are cleaved by NS6<sup>pro</sup>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 04:08:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/626466"], "description"=>"<p>(A) Cartoon representation of the MNV NS6<sup>pro</sup> structure. The N and C-terminal domains are coloured green and orange respectively. The side-chains of the amino acids that make up the catalytic triad, A139 (mutated from Cys), H30 and D54, are shown as sticks. A disordered loop formed by residues 124–130 (residues 124–131 in chain B) is indicated as a dashed line. The peptide bound to NS6<sup>pro</sup> is not shown in this representation. (B) Overlay of HuNV NS6 protease structures from Chiba (PDB-ID: 1WQS), Norwalk (PDB-ID: 2FYQ) and Southampton (PDB-ID: 2IPH) viruses <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038723#pone.0038723-Nakamura1\" target=\"_blank\">[19]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038723#pone.0038723-Zeitler1\" target=\"_blank\">[22]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038723#pone.0038723-Hussey1\" target=\"_blank\">[23]</a>. Excluding the variable C-termini, the root mean square deviations of the backbone atoms of Chiba, Norwalk and Southampton virus NS6<sup>pro</sup> from MNV NS6<sup>pro</sup> are 0.62, 0.43 and 0.41 respectively. The disordered C-terminus of the Chibavirus protease is shown as a dashed line. (C) Structure of FMDV 3C<sup>pro</sup> (PDB-ID: 2J92) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038723#pone.0038723-Sweeney1\" target=\"_blank\">[26]</a>, coloured as in panel (A).</p>", "links"=>[], "tags"=>["mnv", "ns6", "protease", "norovirus", "foot-and-mouth"], "article_id"=>296953, "categories"=>["Virology", "Biochemistry", "Infectious Diseases"], "users"=>["Eoin N. Leen", "Gabriela Baeza", "Stephen Curry"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0038723.g001", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_comparison_of_the_MNV_NS6_protease_with_human_norovirus_NS6_pro_and_foot_and_mouth_disease_virus_3C_pro_/296953", "title"=>"Structural comparison of the MNV NS6 protease with human norovirus NS6<sup>pro</sup> and foot-and-mouth disease virus 3C<sup>pro</sup>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 04:07:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/626659"], "description"=>"<p>The N-terminal and C-terminal β-barrel domains of each protease are coloured green and orange respectively. (A) Binding of residues P5–P1 (C-terminus of NS6<sup>pro</sup>), shown as sticks colour-coded by atom type (Carbon – light-blue; Oxygen – red; Nitrogen – blue), within the peptide binding grove of MNV NS6<sup>pro</sup>. Selected side-chains from the protease are also shown as sticks. Hydrogen bonds and salt-bridges mentioned in the text are indicated by black dashed lines; all such bonds shown are ≤3.1 Å. (B) Same view as in A but showing the surface of MNV NS6<sup>pro</sup>. (C) Binding of residues P5–P1 from a peptide-like inhibitor to SV (a human norovirus) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038723#pone.0038723-Hussey1\" target=\"_blank\">[23]</a>. Water molecules involved in the protease-peptide interaction are shown as red spheres. (D) Same view as in B but showing the surface of SV NS6<sup>pro</sup>. (E) The refined σ-weighted 2F<sub>o</sub>-F<sub>c</sub> map electron density (where F<sub>o</sub> and F<sub>c</sub> are the observed and calculated structure factors respectively) for an A-chain C-terminal peptide, shown at 1.5 σ. (F) The interaction between residues P6–P1 of a peptide ‘product’ and CAV 3C<sup>pro </sup><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038723#pone.0038723-Lu1\" target=\"_blank\">[30]</a>.</p>", "links"=>[], "tags"=>["protease-peptide", "interactions", "residues", "mnv", "sv", "cav"], "article_id"=>297144, "categories"=>["Virology", "Biochemistry", "Infectious Diseases"], "users"=>["Eoin N. Leen", "Gabriela Baeza", "Stephen Curry"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0038723.g003", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_analysis_of_protease_peptide_interactions_for_the_P6_P1_residues_in_MNV_and_SV_NS6_pro_and_CAV_3C_pro_/297144", "title"=>"Comparative analysis of protease-peptide interactions for the P6–P1 residues in MNV and SV NS6<sup>pro</sup> and CAV 3C<sup>pro</sup>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 04:08:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/626547"], "description"=>"<p>(A) Crystal packing of A and B chains of MNV NS6<sup>pro</sup>. The A and B chains of one asymmetric unit are shown along with the neighbouring molecules (labelled A' and B') into which they insert their C-termini. (B) This panel shows the same molecules that are depicted in panel A (with the same colouring) but in this case the A and B chains within the asymmetric unit are superposed; this reveals the very different contacts that they make with their closest neighbour in the crystal. (C) Here the A' and B' chains from panel A are now superposed in order to show the similarity of the conformations of the bound C-termini (shown as sticks) from the A and B chains respectively. Colour-coding is the same as panel A.</p>", "links"=>[], "tags"=>["packing", "mnv", "chains", "asymmetric"], "article_id"=>297042, "categories"=>["Virology", "Biochemistry", "Infectious Diseases"], "users"=>["Eoin N. Leen", "Gabriela Baeza", "Stephen Curry"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0038723.g002", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variations_in_the_crystal_packing_of_the_MNV_NS6_pro_A_and_B_chains_in_the_asymmetric_unit_/297042", "title"=>"Variations in the crystal packing of the MNV NS6<sup>pro</sup> A and B chains in the asymmetric unit.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 04:07:50"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Microbiology", "average_usage"=>[339, 580, 709, 814, 907, 1003, 1095, 1190, 1286, 1375, 1466, 1546, 1622, 1694, 1765, 1830, 1902, 1978, 2054, 2122, 2194, 2269, 2330, 2388, 2460]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[331, 557, 677, 777, 868, 960, 1050, 1136, 1223, 1307, 1390, 1466, 1536, 1603, 1673, 1741, 1814, 1889, 1954, 2028, 2096, 2164, 2233, 2305, 2362]}, {"subject_area"=>"/Medicine and health sciences/Pathology and laboratory medicine", "average_usage"=>[321, 553, 683, 785, 880, 973, 1072, 1162, 1249, 1336, 1425, 1504, 1574, 1642, 1711, 1785, 1852, 1923, 1987, 2050, 2129, 2192, 2259, 2325, 2393]}, {"subject_area"=>"/Physical sciences/Materials science", "average_usage"=>[314, 504, 614, 722, 798, 877, 957, 1055, 1131, 1207, 1278, 1350, 1430, 1503, 1570, 1640, 1694, 1774, 1844, 1915, 1971, 2046, 2104, 2175, 2251]}, {"subject_area"=>"/Physical sciences/Physics", "average_usage"=>[298, 476, 578, 665, 743, 821, 891, 962, 1036, 1108, 1174, 1240, 1312, 1371, 1430, 1494, 1551, 1609, 1673, 1736, 1795, 1857, 1913, 1976, 2035]}]}
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