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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Structural Characterization of the 1918 Influenza Virus H1N1 Neuraminidase<xref ref-type="fn" rid="fn2">▿</xref> </title><author><name sortKey="Xu, Xiaojin" sort="Xu, Xiaojin" uniqKey="Xu X" first="Xiaojin" last="Xu">Xiaojin Xu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zhu, Xueyong" sort="Zhu, Xueyong" uniqKey="Zhu X" first="Xueyong" last="Zhu">Xueyong Zhu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Dwek, Raymond A" sort="Dwek, Raymond A" uniqKey="Dwek R" first="Raymond A." last="Dwek">Raymond A. Dwek</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Stevens, James" sort="Stevens, James" uniqKey="Stevens J" first="James" last="Stevens">James Stevens</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Wilson, Ian A" sort="Wilson, Ian A" uniqKey="Wilson I" first="Ian A." last="Wilson">Ian A. Wilson</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18715929</idno><idno type="pmc">2573172</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2573172</idno><idno type="RBID">PMC:2573172</idno><idno type="doi">10.1128/JVI.00959-08</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000363</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000363</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Structural Characterization of the 1918 Influenza Virus H1N1 Neuraminidase<xref ref-type="fn" rid="fn2">▿</xref> </title><author><name sortKey="Xu, Xiaojin" sort="Xu, Xiaojin" uniqKey="Xu X" first="Xiaojin" last="Xu">Xiaojin Xu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zhu, Xueyong" sort="Zhu, Xueyong" uniqKey="Zhu X" first="Xueyong" last="Zhu">Xueyong Zhu</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Dwek, Raymond A" sort="Dwek, Raymond A" uniqKey="Dwek R" first="Raymond A." last="Dwek">Raymond A. Dwek</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Stevens, James" sort="Stevens, James" uniqKey="Stevens J" first="James" last="Stevens">James Stevens</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Wilson, Ian A" sort="Wilson, Ian A" uniqKey="Wilson I" first="Ian A." last="Wilson">Ian A. Wilson</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">Journal of Virology</title><idno type="ISSN">0022-538X</idno><idno type="eISSN">1098-5514</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Influenza virus neuraminidase (NA) plays a crucial role in facilitating the spread of newly synthesized virus in the host and is an important target for controlling disease progression. The NA crystal structure from the 1918 “Spanish flu” (A/Brevig Mission/1/18 H1N1) and that of its complex with zanamivir (Relenza) at 1.65-Å and 1.45-Å resolutions, respectively, corroborated the successful expression of correctly folded NA tetramers in a baculovirus expression system. An additional cavity adjacent to the substrate-binding site is observed in N1, compared to N2 and N9 NAs, including H5N1. This cavity arises from an open conformation of the 150 loop (Gly147 to Asp151) and appears to be conserved among group 1 NAs (N1, N4, N5, and N8). It closes upon zanamivir binding. Three calcium sites were identified, including a novel site that may be conserved in N1 and N4. Thus, these high-resolution structures, combined with our recombinant expression system, provide new opportunities to augment the limited arsenal of therapeutics against influenza.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">J Virol</journal-id><journal-id journal-id-type="publisher-id">jvi</journal-id><journal-title>Journal of Virology</journal-title><issn pub-type="ppub">0022-538X</issn><issn pub-type="epub">1098-5514</issn><publisher><publisher-name>American Society for Microbiology (ASM)</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">18715929</article-id><article-id pub-id-type="pmc">2573172</article-id><article-id pub-id-type="publisher-id">0959-08</article-id><article-id pub-id-type="doi">10.1128/JVI.00959-08</article-id><article-categories><subj-group subj-group-type="heading"><subject>Structure and Assembly</subject></subj-group></article-categories><title-group><article-title>Structural Characterization of the 1918 Influenza Virus H1N1 Neuraminidase<xref ref-type="fn" rid="fn2">▿</xref> </article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Xiaojin</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff1">3</xref></contrib><contrib contrib-type="author"><name><surname>Zhu</surname><given-names>Xueyong</given-names></name><xref ref-type="aff" rid="aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Dwek</surname><given-names>Raymond A.</given-names></name><xref ref-type="aff" rid="aff1">3</xref></contrib><contrib contrib-type="author"><name><surname>Stevens</surname><given-names>James</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="fn1">†</xref></contrib><contrib contrib-type="author"><name><surname>Wilson</surname><given-names>Ian A.</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff1">2</xref><xref ref-type="corresp" rid="cor1">*</xref></contrib></contrib-group><aff id="aff1">Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037,<label>1</label> Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037,<label>2</label> Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom<label>3</label></aff><author-notes><fn id="cor1"><label>*</label><p>Corresponding author. Mailing address: Department of Molecular Biology BCC206, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037. Phone: (858) 784-2939. Fax: (858) 784-2080. E-mail: <email>wilson@scripps.edu</email></p></fn><fn id="fn1"><label>†</label><p>Present address: Molecular Virology and Vaccines Branch, Influenza Division, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333.</p></fn></author-notes><pub-date pub-type="ppub"><month>11</month><year>2008</year></pub-date><pub-date pub-type="epub"><day>20</day><month>8</month><year>2008</year></pub-date><volume>82</volume><issue>21</issue><fpage>10493</fpage><lpage>10501</lpage><history><date date-type="received"><day>8</day><month>5</month><year>2008</year></date><date date-type="accepted"><day>5</day><month>8</month><year>2008</year></date></history><permissions><copyright-statement>Copyright © 2008, American Society for Microbiology</copyright-statement></permissions><self-uri xlink:title="pdf" xlink:href="zjv02108010493.pdf"></self-uri><abstract><p>Influenza virus neuraminidase (NA) plays a crucial role in facilitating the spread of newly synthesized virus in the host and is an important target for controlling disease progression. The NA crystal structure from the 1918 “Spanish flu” (A/Brevig Mission/1/18 H1N1) and that of its complex with zanamivir (Relenza) at 1.65-Å and 1.45-Å resolutions, respectively, corroborated the successful expression of correctly folded NA tetramers in a baculovirus expression system. An additional cavity adjacent to the substrate-binding site is observed in N1, compared to N2 and N9 NAs, including H5N1. This cavity arises from an open conformation of the 150 loop (Gly147 to Asp151) and appears to be conserved among group 1 NAs (N1, N4, N5, and N8). It closes upon zanamivir binding. Three calcium sites were identified, including a novel site that may be conserved in N1 and N4. Thus, these high-resolution structures, combined with our recombinant expression system, provide new opportunities to augment the limited arsenal of therapeutics against influenza.</p></abstract></article-meta></front><floats-wrap><fig position="float" id="f1"><label>FIG. 1.</label><caption><p>Crystal structure of the 1918 N1 NA tetramer in schematic representation, as viewed from above the viral surface. The tetramer is composed of four identical monomers. One monomer is colored using a rainbow gradient to illustrate the canonical β-propeller arrangement with six four-stranded, antiparallel β-sheets. The active site is located on top of the molecule (membrane distal), close to the local, pseudosixfold symmetry axis. Calcium ions are shown in magenta and glycans in gold. The new calcium ion binding site is highlighted in blue.</p></caption><graphic xlink:href="zjv0210811440001"></graphic></fig><fig position="float" id="f2"><label>FIG. 2.</label><caption><p>Stereo image of superposed monomeric NAs from N1, N4, and N8 in ribbon presentation: N1 in gray, N4 in orange, and N8 in teal. The major variations are located in loop regions: loop A (residues 328 to 347), loop B (354 to 360), loop C (380 to 392), and loop D (450 to 455).</p></caption><graphic xlink:href="zjv0210811440002"></graphic></fig><fig position="float" id="f3"><label>FIG. 3.</label><caption><p>Molecular surfaces of the 18NA active site with and without the binding of zanamivir. (A) Native structure showing the large 150 cavity that is unoccupied close to the zanamivir binding site. (B) Inhibitor-bound structure, in which structural changes bring the 150 loop proximal to the zanamivir binding site and, therefore, close the 150 cavity.</p></caption><graphic xlink:href="zjv0210811440003"></graphic></fig><fig position="float" id="f4"><label>FIG. 4.</label><caption><p>The 150 cavity of the native 18NA structure. (A) Electrostatic potential of the zanamivir binding site and the 150 cavity. Negatively charged regions are red, positively charged regions are blue, and neutral regions are whitish. (B) Residues bordering the pocket are shown with their side chains. For both images, zanamivir from the complex structure was superimposed onto the native 18NA structure in order to illustrate the extra binding pocket before the conformational changes are induced by inhibitor binding. Both images are viewed in the same orientation with the 150 cavity in the center.</p></caption><graphic xlink:href="zjv0210811440004"></graphic></fig><fig position="float" id="f5"><label>FIG. 5.</label><caption><p>Stereo view of the active sites of the superimposed zanamivir-bound (green) and unbound (gray) structures of 18NA. Conserved charged residues, Arg118, Asp151, Arg152, Arg224, Glu276, Arg292, and Arg371, as well as the structurally conserved water molecule involved in the direct interactions with the inhibitor, are shown in ball-and-stick representation. Val 149 in the 150 loop, in which the major conformational changes occur upon inhibitor binding, is also highlighted in stick presentation to illustrate the extent of the loop rearrangement.</p></caption><graphic xlink:href="zjv0210811440005"></graphic></fig><fig position="float" id="f6"><label>FIG. 6.</label><caption><p>Active site of 18NA, showing the bound zanamivir with the σ<sub>A</sub>-weighted 2<italic>F</italic><sub>obs</sub> − <italic>F</italic><sub>calc</sub> electron density map contoured at 2.0 σ.</p></caption><graphic xlink:href="zjv0210811440006"></graphic></fig><fig position="float" id="f7"><label>FIG. 7.</label><caption><p>Calcium-binding sites in 18NA. (A) The calcium (site 2) at the molecular fourfold axis (i.e., crystallographic twofold axis). Only two monomers are shown for clarity, and side chains are labeled (A and B) after residue number to distinguish two monomers in the asymmetric unit. The coordination of the calcium ion is shown by black dashed lines, and hydrogen bonds are shown with green dashed lines. (B) The new calcium binding site 3, highlighting the side chains of Asp379, Asn381, and Asp387; the main-chain carbonyl of Ser389; and two water molecules in direct contact with the calcium ion.</p></caption><graphic xlink:href="zjv0210811440007"></graphic></fig><table-wrap position="float" id="t1"><label>TABLE 1.</label><caption><p>Data collection and refinement statistics of the crystal structures of A/Brevig Mission/1/1918 N1 NA and its complex with zanamivir</p></caption><table frame="hsides" rules="groups"><thead><tr><th colspan="1" rowspan="2" align="center" valign="middle">Parameter</th><th colspan="2" rowspan="1" align="center" valign="bottom">Result<xref ref-type="table-fn" rid="t1fn1"><italic>a</italic></xref> for:
<hr></hr></th></tr><tr><th colspan="1" rowspan="1" align="center" valign="bottom">1918 NA</th><th colspan="1" rowspan="1" align="center" valign="bottom">1918 NA + zanamivir</th></tr></thead><tbody><tr><td colspan="1" rowspan="1" align="left" valign="top">Data collection</td><td colspan="1" rowspan="1" align="left" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top"></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Space group</td><td colspan="1" rowspan="1" align="left" valign="top">C222<sub>1</sub></td><td colspan="1" rowspan="1" align="left" valign="top">C222<sub>1</sub></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Cell dimensions</td><td colspan="1" rowspan="1" align="left" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top"></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> a, b, c (Å)</td><td colspan="1" rowspan="1" align="left" valign="top">117.73, 138.47, 117.86</td><td colspan="1" rowspan="1" align="left" valign="top">118.04, 129.25, 118.85</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> α, β, γ (°)</td><td colspan="1" rowspan="1" align="left" valign="top">90, 90, 90</td><td colspan="1" rowspan="1" align="left" valign="top">90, 90, 90</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Resolution range (Å)</td><td colspan="1" rowspan="1" align="left" valign="top">50.00-1.65 (1.68-1.65)</td><td colspan="1" rowspan="1" align="left" valign="top">50.00-1.45 (1.49-1.45)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Unique reflections</td><td colspan="1" rowspan="1" align="left" valign="top">113,144 (4,405)</td><td colspan="1" rowspan="1" align="left" valign="top">155,978 (11,401)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Completeness (%)</td><td colspan="1" rowspan="1" align="left" valign="top">97.3 (76.4)</td><td colspan="1" rowspan="1" align="left" valign="top">97.6 (86.3)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Redundancy</td><td colspan="1" rowspan="1" align="left" valign="top">4.2 (2.8)</td><td colspan="1" rowspan="1" align="left" valign="top">6.8 (5.6)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Wilson <italic>B</italic> value (Å<sup>2</sup>)</td><td colspan="1" rowspan="1" align="left" valign="top">16.3</td><td colspan="1" rowspan="1" align="left" valign="top">12.0</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"><italic>R</italic><sub>sym</sub><xref ref-type="table-fn" rid="t1fn2"><italic>b</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">0.09 (0.53)</td><td colspan="1" rowspan="1" align="left" valign="top">0.07 (0.46)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"><<italic>I</italic>/σ></td><td colspan="1" rowspan="1" align="left" valign="top">22.2 (2.0)</td><td colspan="1" rowspan="1" align="left" valign="top">23.9 (2.7)</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Refinement</td><td colspan="1" rowspan="1" align="left" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top"></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"><italic>R</italic><sub>cryst</sub><xref ref-type="table-fn" rid="t1fn3"><italic>c</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">0.18</td><td colspan="1" rowspan="1" align="left" valign="top">0.14</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"><italic>R</italic><sub>free</sub><xref ref-type="table-fn" rid="t1fn4"><italic>d</italic></xref></td><td colspan="1" rowspan="1" align="left" valign="top">0.21</td><td colspan="1" rowspan="1" align="left" valign="top">0.16</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Molecules in asymmetric unit</td><td colspan="1" rowspan="1" align="left" valign="top">2 monomers</td><td colspan="1" rowspan="1" align="left" valign="top">2 monomers</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">RMSD from ideal</td><td colspan="1" rowspan="1" align="left" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top"></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Bond length (Å)</td><td colspan="1" rowspan="1" align="left" valign="top">0.013</td><td colspan="1" rowspan="1" align="left" valign="top">0.013</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Bond angle (°)</td><td colspan="1" rowspan="1" align="left" valign="top">1.44</td><td colspan="1" rowspan="1" align="left" valign="top">1.44</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Avg <italic>B</italic> values (Å<sup>2</sup>)</td><td colspan="1" rowspan="1" align="left" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top"></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Protein</td><td colspan="1" rowspan="1" align="left" valign="top">16.6</td><td colspan="1" rowspan="1" align="left" valign="top">10.9</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Inhibitor</td><td colspan="1" rowspan="1" align="left" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">8.6/9.2<xref ref-type="table-fn" rid="t1fn5"><italic>e</italic></xref></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Water</td><td colspan="1" rowspan="1" align="left" valign="top">32.0</td><td colspan="1" rowspan="1" align="left" valign="top">28.3</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top">Ramachandran plot (%)</td><td colspan="1" rowspan="1" align="left" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top"></td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Most favored</td><td colspan="1" rowspan="1" align="left" valign="top">84.3</td><td colspan="1" rowspan="1" align="left" valign="top">84.6</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Additionally allowed</td><td colspan="1" rowspan="1" align="left" valign="top">15.1</td><td colspan="1" rowspan="1" align="left" valign="top">14.8</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Generously allowed</td><td colspan="1" rowspan="1" align="left" valign="top">0.6</td><td colspan="1" rowspan="1" align="left" valign="top">0.6</td></tr><tr><td colspan="1" rowspan="1" align="left" valign="top"> Disallowed</td><td colspan="1" rowspan="1" align="left" valign="top">0.0</td><td colspan="1" rowspan="1" align="left" valign="top">0.0</td></tr></tbody></table><table-wrap-foot><fn id="t1fn1"><label>a</label><p>Values in parentheses are for the highest-resolution shell.</p></fn><fn id="t1fn2"><label>b</label><p><italic>R</italic><sub>sym</sub> = <inline-formula><tex-math id="M1">\documentclass[10pt]{article}
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\begin{equation*}{\Sigma}_{{\mathit{hkl}}}{\Sigma}_{{\mathit{i}}}{\vert}{\mathit{I}}_{{\mathit{i}}}({\mathit{hkl}})-<{\mathit{I}}_{{\mathit{i}}}({\mathit{hkl}}){\mathit{mh}};-3{\mathit{q}}>{\vert}/{\Sigma}_{{\mathit{hkl}}}{\Sigma}_{{\mathit{i}}}{\vert}{\mathit{I}}_{{\mathit{i}}}({\mathit{hkl}}){\vert}\end{equation*}\end{document}</tex-math></inline-formula>.</p></fn><fn id="t1fn3"><label>c</label><p><italic>R</italic><sub>cryst</sub> = <inline-formula><tex-math id="M2">\documentclass[10pt]{article}
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\begin{equation*}{\Sigma}_{{\mathit{hkl}}}{\vert}{\vert}{\mathit{F}}_{{\mathit{o}}}({\mathit{hkl}}){\vert}-{\vert}{\mathit{F}}_{{\mathit{c}}}({\mathit{hkl}}){\vert}{\vert}/{\Sigma}_{{\mathit{hkl}}}{\vert}{\mathit{F}}_{{\mathit{o}}}({\mathit{hkl}}){\vert}\end{equation*}\end{document}</tex-math></inline-formula>.</p></fn><fn id="t1fn4"><label>d</label><p><italic>R</italic><sub>free</sub> is calculated as for <italic>R</italic><sub>cryst</sub>, but from 5% of the data that were excluded from the refinement.</p></fn><fn id="t1fn5"><label>e</label><p>Values are for the two ligands per asymmetric unit.</p></fn></table-wrap-foot></table-wrap><table-wrap position="float" id="t2"><label>TABLE 2.</label><caption><p>Comparison of peptide sequences of influenza A virus NAs of N1 and N4 subtypes in the regions of the putative calcium binding site<xref ref-type="table-fn" rid="t2fn1"><italic>a</italic></xref></p></caption><table frame="hsides" rules="groups"><tbody><tr><td colspan="1" rowspan="1" align="center" valign="top"><graphic xlink:href="zjv0210811440008.jpg"></graphic></td></tr></tbody></table><table-wrap-foot><fn id="t2fn1"><label>a</label><p>Residues involved in the direct interaction with the calcium ion are shown in red, and pink indicates residues in which only the backbone carbonyl is involved in the interactions with the calcium ion. Green indicates residues surrounding the site which are structurally important.</p></fn></table-wrap-foot></table-wrap></floats-wrap></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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