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1ddl

From Proteopedia

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[[Image:1ddl.gif|left|200px]]<br /><applet load="1ddl" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ddl, resolution 2.7&Aring;" />
 
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'''DESMODIUM YELLOW MOTTLE TYMOVIRUS'''<br />
 
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==Overview==
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==DESMODIUM YELLOW MOTTLE TYMOVIRUS==
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Desmodium yellow mottle virus is a 28 nm diameter, T=3 icosahedral plant virus of the tymovirus group. Its structure has been solved to a resolution of 2.7 A using X-ray diffraction analysis based on molecular replacement and phase extension methods. The final R value was 0.151 (R(free)=0.159) for 134,454 independent reflections. The folding of the polypeptide backbone is nearly identical with that of turnip yellow mosaic virus, as is the arrangement of subunits in the virus capsid. However, a major difference in the disposition of the amino-terminal ends of the subunits was observed. In turnip yellow mosaic virus, those from the B and C subunits comprising the hexameric capsomeres formed an annulus about the interior of the capsomere, while the corresponding N termini of the pentameric capsomere A subunits were not visible at all in electron density maps. In Desmodium yellow mottle tymovirus, amino termini from the A and B subunits combine to form the annuli, thereby resulting in a much strengthened association between the two types of capsomeres and an, apparently, more stable capsid. The first 13 residues of the C subunit were invisible in electron density maps. Two ordered fragments of single-stranded RNA, seven and two nucleotides in length, were observed. The ordered water structure of the virus particle was delineated and required 95 solvent molecules per protein subunit.
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<StructureSection load='1ddl' size='340' side='right'caption='[[1ddl]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1ddl]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Desmodium_yellow_mottle_virus Desmodium yellow mottle virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DDL FirstGlance]. <br>
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1DDL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desmodium_yellow_mottle_virus Desmodium yellow mottle virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DDL OCA].
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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]] 2.7&#8491;</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=1ddl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ddl OCA], [https://pdbe.org/1ddl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ddl RCSB], [https://www.ebi.ac.uk/pdbsum/1ddl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ddl ProSAT]</span></td></tr>
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==Reference==
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</table>
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Refined structure of desmodium yellow mottle tymovirus at 2.7 A resolution., Larson SB, Day J, Canady MA, Greenwood A, McPherson A, J Mol Biol. 2000 Aug 18;301(3):625-42. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10966774 10966774]
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== Function ==
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[https://www.uniprot.org/uniprot/O89511_9VIRU O89511_9VIRU]
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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/dd/1ddl_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=1ddl ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Desmodium yellow mottle virus]]
[[Category: Desmodium yellow mottle virus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Canady, M A.]]
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[[Category: Canady MA]]
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[[Category: Day, J.]]
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[[Category: Day J]]
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[[Category: Greenwood, A.]]
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[[Category: Greenwood A]]
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[[Category: Larson, S B.]]
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[[Category: Larson SB]]
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[[Category: McPherson, A.]]
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[[Category: McPherson A]]
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[[Category: capsid protein]]
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[[Category: coat protein]]
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[[Category: dymv]]
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[[Category: icosahedral virus]]
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[[Category: plant virus]]
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[[Category: rna]]
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[[Category: tymoviruses]]
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[[Category: water structure]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:15:37 2008''
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Current revision

DESMODIUM YELLOW MOTTLE TYMOVIRUS

PDB ID 1ddl

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