1ddl: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<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>
<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>
</td></tr><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>
</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>
<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>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O89511_9VIRU O89511_9VIRU]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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].
</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>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:10966774<ref>PMID:10966774</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ddl" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Desmodium yellow mottle virus]]
[[Category: Desmodium yellow mottle virus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Canady, M A]]
[[Category: Canady MA]]
[[Category: Day, J]]
[[Category: Day J]]
[[Category: Greenwood, A]]
[[Category: Greenwood A]]
[[Category: Larson, S B]]
[[Category: Larson SB]]
[[Category: McPherson, A]]
[[Category: McPherson A]]
[[Category: Capsid protein]]
[[Category: Coat protein]]
[[Category: Dymv]]
[[Category: Icosahedral virus]]
[[Category: Plant virus]]
[[Category: Rna]]
[[Category: Tymoviruse]]
[[Category: Virus-rna complex]]
[[Category: Water structure]]

Latest revision as of 09:52, 7 February 2024

DESMODIUM YELLOW MOTTLE TYMOVIRUSDESMODIUM YELLOW MOTTLE TYMOVIRUS

Structural highlights

1ddl is a 5 chain structure with sequence from Desmodium yellow mottle virus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.7Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O89511_9VIRU

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1ddl, resolution 2.70Å

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
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