2zi0

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Tav2b/siRNA complex

Structural highlights

2zi0 is a 4 chain structure with sequence from Tomato aspermy virus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.82Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

2B_TAV Acts as suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. Forms a homodimer to measure siRNA duplex in a length-preferencemode. Binds to both siRNA duplexes (19bp) and long siRNA duplexes (30bp).^[1] ^[2] ^[3]

Evolutionary Conservation

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

Publication Abstract from PubMed

The 2b proteins encoded by cucumovirus act as post-transcriptional gene silencing suppressors to counter host defence during infection. Here we report the crystal structure of Tomato aspermy virus 2b (TAV2b) protein bound to a 19 bp small interfering RNA (siRNA) duplex. TAV2b adopts an all alpha-helix structure and forms a homodimer to measure siRNA duplex in a length-preference mode. TAV2b has a pair of hook-like structures to recognize simultaneously two alpha-helical turns of A-form RNA duplex by fitting its alpha-helix backbone into two adjacent major grooves of siRNA duplex. The conserved pi-stackings between tryptophan and the 5'-terminal base of siRNA duplex from both ends enhance the recognition. TAV2b further oligomerizes to form a dimer of dimers through the conserved leucine-zipper-like motif at its amino-terminal alpha-helix. Biochemical experiments suggest that TAV2b might interfere with the post-transcriptional gene silencing pathway by directly binding to siRNA duplex.

Structural basis for RNA-silencing suppression by Tomato aspermy virus protein 2b.,Chen HY, Yang J, Lin C, Yuan YA EMBO Rep. 2008 Aug;9(8):754-60. Epub 2008 Jul 4. PMID:18600235^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Li HW, Lucy AP, Guo HS, Li WX, Ji LH, Wong SM, Ding SW. Strong host resistance targeted against a viral suppressor of the plant gene silencing defence mechanism. EMBO J. 1999 May 17;18(10):2683-91. PMID:10329615 doi:http://dx.doi.org/10.1093/emboj/18.10.2683
↑ Ding SW, Anderson BJ, Haase HR, Symons RH. New overlapping gene encoded by the cucumber mosaic virus genome. Virology. 1994 Feb;198(2):593-601. PMID:8291242 doi:http://dx.doi.org/10.1006/viro.1994.1071
↑ Shi BJ, Ding SW, Symons RH. In vivo expression of an overlapping gene encoded by the cucumoviruses. J Gen Virol. 1997 Jan;78 ( Pt 1):237-41. PMID:9010309
↑ Chen HY, Yang J, Lin C, Yuan YA. Structural basis for RNA-silencing suppression by Tomato aspermy virus protein 2b. EMBO Rep. 2008 Aug;9(8):754-60. Epub 2008 Jul 4. PMID:18600235 doi:10.1038/embor.2008.118

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2zi0"

Categories: Large Structures | Tomato aspermy virus | Chen H-Y | Yuan YA

@@ Line 1: / Line 1: @@
 ==Crystal structure of Tav2b/siRNA complex==
-<StructureSection load='2zi0' size='340' side='right' caption='[[2zi0]], [[Resolution|resolution]] 2.82&Aring;' scene=''>
+<StructureSection load='2zi0' size='340' side='right'caption='[[2zi0]], [[Resolution|resolution]] 2.82&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zi0]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chrysanthemum_aspermy_virus Chrysanthemum aspermy virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZI0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZI0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zi0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Tomato_aspermy_virus Tomato aspermy virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZI0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZI0 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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]] 2.82&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RNA4A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12315 Chrysanthemum aspermy virus])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zi0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zi0 OCA], [http://pdbe.org/2zi0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zi0 RCSB], [http://www.ebi.ac.uk/pdbsum/2zi0 PDBsum]</span></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=2zi0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zi0 OCA], [https://pdbe.org/2zi0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zi0 RCSB], [https://www.ebi.ac.uk/pdbsum/2zi0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zi0 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/2B_TAV 2B_TAV]] Acts as suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. Forms a homodimer to measure siRNA duplex in a length-preferencemode. Binds to both siRNA duplexes (19bp) and long siRNA duplexes (30bp).<ref>PMID:10329615</ref> <ref>PMID:8291242</ref> <ref>PMID:9010309</ref>
+[https://www.uniprot.org/uniprot/2B_TAV 2B_TAV] Acts as suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. Forms a homodimer to measure siRNA duplex in a length-preferencemode. Binds to both siRNA duplexes (19bp) and long siRNA duplexes (30bp).<ref>PMID:10329615</ref> <ref>PMID:8291242</ref> <ref>PMID:9010309</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zi/2zi0_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zi/2zi0_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 35: / Line 36: @@
 *[[Suppression of RNA Silencing by Viruses|Suppression of RNA Silencing by Viruses]]
 *[[Tomato aspermy virus protein 2b Suppression of RNA Silencing|Tomato aspermy virus protein 2b Suppression of RNA Silencing]]
-*[[User:Wayne Decatur/Flock house virus B2 protein Suppression of RNA Silencing|User:Wayne Decatur/Flock house virus B2 protein Suppression of RNA Silencing]]
-*[[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]]
-*[[User:Wayne Decatur/Suppression of RNA Silencing by Viruses|User:Wayne Decatur/Suppression of RNA Silencing by Viruses]]
-*[[User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing|User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing]]
-*[[User:Wayne Decatur/UNH CME Workshop March 11 2011|User:Wayne Decatur/UNH CME Workshop March 11 2011]]
-*[[User:Wayne Decatur/UNH Seminar Feb 1st 2011|User:Wayne Decatur/UNH Seminar Feb 1st 2011]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Chrysanthemum aspermy virus]]
+[[Category: Large Structures]]
-[[Category: Chen, H Y]]
+[[Category: Tomato aspermy virus]]
-[[Category: Yuan, Y A]]
+[[Category: Chen H-Y]]
-[[Category: Gene regulation-rna complex]]
+[[Category: Yuan YA]]
-[[Category: Nucleus]]
-[[Category: Rnai suppression]]
-[[Category: Suppressor of rna silencing]]

2zi0

From Proteopedia

Current revision

Crystal structure of Tav2b/siRNA complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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