1c8n

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(New page: 200px<br /><applet load="1c8n" size="450" color="white" frame="true" align="right" spinBox="true" caption="1c8n, resolution 2.25&Aring;" /> '''TOBACCO NECROSIS VIR...)
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[[Image:1c8n.gif|left|200px]]<br /><applet load="1c8n" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1c8n, resolution 2.25&Aring;" />
 
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'''TOBACCO NECROSIS VIRUS'''<br />
 
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==Overview==
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==TOBACCO NECROSIS VIRUS==
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The crystal structure of tobacco necrosis virus (TNV) has been determined, by real-space averaging with 5-fold non-crystallographic symmetry, and, refined to R=25.3 % for diffraction data to 2.25 A resolution. A total of, 180 subunits form a T=3 virus shell with a diameter of about 280 A and a, small protrusion at the 5-fold axis. In 276 amino acid residues, the, respective amino terminal 86, 87 and 56 residues of the A, B and C, subunits are disordered. No density for the RNA was found. The subunits, have a "jelly roll" beta-barrel structure, as have the structures of the, subunits of other spherical viruses. The tertiary and quaternary, structures of TNV are, in particular, similar to those of southern bean, mosaic virus, although they are classified in different groups. Invisible, residues 1 to 56 with a high level of basic residues are considered to be, located inside the particle. Sequence comparison of the coat proteins of, several TNV strains showed that the sequences of the disordered segment, diverge considerably as compared with those of the ordered segment, consistent with a small tertiary structural constraint being imposed on, the N-terminal segment. Basic residues are localized on the subunit, interfaces or inner surface of the capsid. Positive charges of the basic, residues facing the interior, as well as those of the N-terminal segment, may neutralize the negative charge of the RNA inside. Five calcium ions, per icosahedral asymmetric unit are located at the subunit interfaces;, three are close to the exterior surface, the other two away from it. The, environments of the first three are similar, and those of the other two, sites are similar. These calcium ions are assumed to be responsible for, the stabilization/transition of the quaternary structure of the shell., Three peptide segments ordered only in the C subunits are clustered around, each 3-fold (quasi-6-fold) axis forming a beta-annulus, and may lead to, quasi-equivalent interactions for the organization of the T=3 shell.
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<StructureSection load='1c8n' size='340' side='right'caption='[[1c8n]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1c8n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Unidentified_tobacco_necrosis_virus Unidentified tobacco necrosis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C8N FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1c8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c8n OCA], [https://pdbe.org/1c8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c8n RCSB], [https://www.ebi.ac.uk/pdbsum/1c8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c8n ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9IPS9_9TOMB Q9IPS9_9TOMB]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c8/1c8n_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1c8n ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of tobacco necrosis virus (TNV) has been determined by real-space averaging with 5-fold non-crystallographic symmetry, and refined to R=25.3 % for diffraction data to 2.25 A resolution. A total of 180 subunits form a T=3 virus shell with a diameter of about 280 A and a small protrusion at the 5-fold axis. In 276 amino acid residues, the respective amino terminal 86, 87 and 56 residues of the A, B and C subunits are disordered. No density for the RNA was found. The subunits have a "jelly roll" beta-barrel structure, as have the structures of the subunits of other spherical viruses. The tertiary and quaternary structures of TNV are, in particular, similar to those of southern bean mosaic virus, although they are classified in different groups. Invisible residues 1 to 56 with a high level of basic residues are considered to be located inside the particle. Sequence comparison of the coat proteins of several TNV strains showed that the sequences of the disordered segment diverge considerably as compared with those of the ordered segment, consistent with a small tertiary structural constraint being imposed on the N-terminal segment. Basic residues are localized on the subunit interfaces or inner surface of the capsid. Positive charges of the basic residues facing the interior, as well as those of the N-terminal segment, may neutralize the negative charge of the RNA inside. Five calcium ions per icosahedral asymmetric unit are located at the subunit interfaces; three are close to the exterior surface, the other two away from it. The environments of the first three are similar, and those of the other two sites are similar. These calcium ions are assumed to be responsible for the stabilization/transition of the quaternary structure of the shell. Three peptide segments ordered only in the C subunits are clustered around each 3-fold (quasi-6-fold) axis forming a beta-annulus, and may lead to quasi-equivalent interactions for the organization of the T=3 shell.
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==About this Structure==
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Crystal structure of tobacco necrosis virus at 2.25 A resolution.,Oda Y, Saeki K, Takahashi Y, Maeda T, Naitow H, Tsukihara T, Fukuyama K J Mol Biol. 2000 Jun 30;300(1):153-69. PMID:10864506<ref>PMID:10864506</ref>
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1C8N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Unidentified_tobacco_necrosis_virus Unidentified tobacco necrosis virus] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1C8N OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure of tobacco necrosis virus at 2.25 A resolution., Oda Y, Saeki K, Takahashi Y, Maeda T, Naitow H, Tsukihara T, Fukuyama K, J Mol Biol. 2000 Jun 30;300(1):153-69. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10864506 10864506]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 1c8n" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Unidentified tobacco necrosis virus]]
[[Category: Unidentified tobacco necrosis virus]]
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[[Category: Fukuyama, K.]]
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[[Category: Fukuyama K]]
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[[Category: Oda, Y.]]
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[[Category: Oda Y]]
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[[Category: CA]]
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[[Category: icosahedral virus]]
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[[Category: virus]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 01:15:27 2007''
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Current revision

TOBACCO NECROSIS VIRUS

PDB ID 1c8n

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