View source for 8xbs


==C. elegans apo-SID1 structure==
<StructureSection load='8xbs' size='340' side='right'caption='[[8xbs]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8xbs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8XBS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8XBS FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.21&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CLR:CHOLESTEROL'>CLR</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=POV:(2S)-3-(HEXADECANOYLOXY)-2-[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL+2-(TRIMETHYLAMMONIO)ETHYL+PHOSPHATE'>POV</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=8xbs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8xbs OCA], [https://pdbe.org/8xbs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8xbs RCSB], [https://www.ebi.ac.uk/pdbsum/8xbs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8xbs ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SID1_CAEEL SID1_CAEEL] Plays a role in RNA-mediated gene silencing by acting cell-autonomously as a channel for the transport of double-stranded RNA (dsRNA) between cells. Mediates the spread of dsRNA and subsequent silencing of genes in cells distant from the site of dsRNA introduction. Selective for dsRNA. Preferentially binds long dsRNA, from 50 base pairs up to 700. Short 20 base-pair long molecules are not bound. May also bind dsDNA, but with lower affinity. Binding may be sequence-independent (PubMed:26067272). Required for avoidance behavior induced by small RNAs derived from pathogenic bacteria such as P.aeruginosa (PubMed:32908307).<ref>PMID:11834782</ref> <ref>PMID:12970568</ref> <ref>PMID:14738731</ref> <ref>PMID:17381285</ref> <ref>PMID:19155320</ref> <ref>PMID:19168628</ref> <ref>PMID:20512143</ref> <ref>PMID:21474576</ref> <ref>PMID:22178129</ref> <ref>PMID:22293577</ref> <ref>PMID:22902558</ref> <ref>PMID:26067272</ref> <ref>PMID:32908307</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The nucleic acid transport properties of the systemic RNAi-defective (SID) 1 family make them attractive targets for developing RNA-based therapeutics and drugs. However, the molecular basis for double-stranded (ds) RNA recognition by SID1 family remains elusive. Here, we report the cryo-EM structures of Caenorhabditis elegans (c) SID1 alone and in complex with dsRNA, both at a resolution of 2.2 A. The dimeric cSID1 interacts with two dsRNA molecules simultaneously. The dsRNA is located at the interface between beta-strand rich domain (BRD)1 and BRD2 and nearly parallel to the membrane plane. In addition to extensive ionic interactions between basic residues and phosphate backbone, several hydrogen bonds are formed between 2'-hydroxyl group of dsRNA and the contact residues. Additionally, the electrostatic potential surface shows three basic regions are fitted perfectly into three major grooves of dsRNA. These structural characteristics enable cSID1 to bind dsRNA in a sequence-independent manner and to distinguish between DNA and RNA. The cSID1 exhibits no conformational changes upon binding dsRNA, with the exception of a few binding surfaces. Structural mapping of dozens of loss-of-function mutations allows potential interpretation of their diverse functional mechanisms. Our study marks an important step toward mechanistic understanding of the SID1 family-mediated dsRNA uptake.

Structural basis for double-stranded RNA recognition by SID1.,Wang R, Cong Y, Qian D, Yan C, Gong D Nucleic Acids Res. 2024 May 14:gkae395. doi: 10.1093/nar/gkae395. PMID:38742627<ref>PMID:38742627</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8xbs" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Caenorhabditis elegans]]
[[Category: Large Structures]]
[[Category: Gong DS]]