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1r9f

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Revision as of 07:54, 28 February 2018

Crystal structure of p19 complexed with 19-bp small interfering RNA

Structural highlights

1r9f is a 3 chain structure with sequence from Tbsv. The February 2008 RCSB PDB Molecule of the Month feature on Small Interfering RNA by David S. Goodsell is 10.2210/rcsb_pdb/mom_2008_2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Gene:	p19 (TBSV)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[P19_TBSVC] Acts as a 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. Binds to short interfering RNAs (siRNAs) with high affinity. Acts as a molecular caliper to specifically select siRNAs based on the length of the duplex region of the RNA (By similarity).

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

RNA silencing (also known as RNA interference) is a conserved biological response to double-stranded RNA that regulates gene expression, and has evolved in plants as a defence against viruses. The response is mediated by small interfering RNAs (siRNAs), which guide the sequence-specific degradation of cognate messenger RNAs. As a counter-defence, many viruses encode proteins that specifically inhibit the silencing machinery. The p19 protein from the tombusvirus is such a viral suppressor of RNA silencing and has been shown to bind specifically to siRNA. Here, we report the 1.85-A crystal structure of p19 bound to a 21-nucleotide siRNA, where the 19-base-pair RNA duplex is cradled within the concave face of a continuous eight-stranded beta-sheet, formed across the p19 homodimer interface. Direct and water-mediated intermolecular contacts are restricted to the backbone phosphates and sugar 2'-OH groups, consistent with sequence-independent p19-siRNA recognition. Two alpha-helical 'reading heads' project from opposite ends of the p19 homodimer and position pairs of tryptophans for stacking over the terminal base pairs, thereby measuring and bracketing both ends of the siRNA duplex. Our structure provides an illustration of siRNA sequestering by a viral protein.

Recognition of small interfering RNA by a viral suppressor of RNA silencing.,Ye K, Malinina L, Patel DJ Nature. 2003 Dec 18;426(6968):874-8. Epub 2003 Dec 3. PMID:14661029^[1]

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

References

↑ Ye K, Malinina L, Patel DJ. Recognition of small interfering RNA by a viral suppressor of RNA silencing. Nature. 2003 Dec 18;426(6968):874-8. Epub 2003 Dec 3. PMID:14661029 doi:http://dx.doi.org/10.1038/nature02213

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/1r9f"

@@ Line 1: / Line 1: @@
 ==Crystal structure of p19 complexed with 19-bp small interfering RNA==
 <StructureSection load='1r9f' size='340' side='right' caption='[[1r9f]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <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>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">p19 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12145 TBSV])</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=1r9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9f OCA], [http://pdbe.org/1r9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r9f RCSB], [http://www.ebi.ac.uk/pdbsum/1r9f PDBsum]</span></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=1r9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r9f OCA], [http://pdbe.org/1r9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r9f RCSB], [http://www.ebi.ac.uk/pdbsum/1r9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1r9f ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r9/1r9f_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r9/1r9f_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1r9f

From Proteopedia

Revision as of 07:54, 28 February 2018

Crystal structure of p19 complexed with 19-bp small interfering RNA

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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