1ddl

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:52, 7 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ddl.gif|left|200px]]
 
-
{{Structure
+
==DESMODIUM YELLOW MOTTLE TYMOVIRUS==
-
|PDB= 1ddl |SIZE=350|CAPTION= <scene name='initialview01'>1ddl</scene>, resolution 2.7&Aring;
+
<StructureSection load='1ddl' size='340' side='right'caption='[[1ddl]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
+
<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>
-
|ACTIVITY=
+
</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>
-
|GENE=
+
<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>
-
|DOMAIN=
+
</table>
-
|RELATEDENTRY=
+
== Function ==
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ddl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ddl OCA], [http://www.ebi.ac.uk/pdbsum/1ddl PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ddl RCSB]</span>
+
[https://www.uniprot.org/uniprot/O89511_9VIRU O89511_9VIRU]
-
}}
+
== Evolutionary Conservation ==
-
 
+
[[Image:Consurf_key_small.gif|200px|right]]
-
'''DESMODIUM YELLOW MOTTLE TYMOVIRUS'''
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
 
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/1ddl_consurf.spt"</scriptWhenChecked>
-
==Overview==
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
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.
+
<text>to colour the structure by Evolutionary Conservation</text>
-
 
+
</jmolCheckbox>
-
==About this Structure==
+
</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].
-
1DDL is a [[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].
+
<div style="clear:both"></div>
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
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://www.ncbi.nlm.nih.gov/pubmed/10966774 10966774]
+
[[Category: Desmodium yellow mottle virus]]
[[Category: Desmodium yellow mottle virus]]
-
[[Category: Single protein]]
+
[[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: water structure]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:39:31 2008''
+

Current revision

DESMODIUM YELLOW MOTTLE TYMOVIRUS

PDB ID 1ddl

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ddl"
Personal tools