9l8m: Difference between revisions

Latest revision as of 20:25, 8 September 2026

Structure of SID-1 in complex with dsRNA

Structural highlights

9l8m is a 3 chain structure with sequence from Caenorhabditis elegans and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.9Å
Ligands:	LBN, NAG, Y01, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13]

References

↑ Winston WM, Molodowitch C, Hunter CP. Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Science. 2002 Mar 29;295(5564):2456-9. PMID:11834782 doi:10.1126/science.1068836
↑ Feinberg EH, Hunter CP. Transport of dsRNA into cells by the transmembrane protein SID-1. Science. 2003 Sep 12;301(5639):1545-7. PMID:12970568 doi:10.1126/science.1087117
↑ Tijsterman M, May RC, Simmer F, Okihara KL, Plasterk RH. Genes required for systemic RNA interference in Caenorhabditis elegans. Curr Biol. 2004 Jan 20;14(2):111-6. PMID:14738731 doi:10.1016/j.cub.2003.12.029
↑ Hunter CP, Winston WM, Molodowitch C, Feinberg EH, Shih J, Sutherlin M, Wright AJ, Fitzgerald MC. Systemic RNAi in Caenorhabditis elegans. Cold Spring Harb Symp Quant Biol. 2006;71:95-100. PMID:17381285 doi:10.1101/sqb.2006.71.060
↑ Shih JD, Fitzgerald MC, Sutherlin M, Hunter CP. The SID-1 double-stranded RNA transporter is not selective for dsRNA length. RNA. 2009 Mar;15(3):384-90. PMID:19155320 doi:10.1261/rna.1286409
↑ Jose AM, Smith JJ, Hunter CP. Export of RNA silencing from C. elegans tissues does not require the RNA channel SID-1. Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2283-8. PMID:19168628 doi:10.1073/pnas.0809760106
↑ Calixto A, Chelur D, Topalidou I, Chen X, Chalfie M. Enhanced neuronal RNAi in C. elegans using SID-1. Nat Methods. 2010 Jul;7(7):554-9. PMID:20512143 doi:10.1038/nmeth.1463
↑ Shih JD, Hunter CP. SID-1 is a dsRNA-selective dsRNA-gated channel. RNA. 2011 Jun;17(6):1057-65. PMID:21474576 doi:10.1261/rna.2596511
↑ Kobayashi I, Tsukioka H, Kômoto N, Uchino K, Sezutsu H, Tamura T, Kusakabe T, Tomita S. SID-1 protein of Caenorhabditis elegans mediates uptake of dsRNA into Bombyx cells. Insect Biochem Mol Biol. 2012 Feb;42(2):148-54. PMID:22178129 doi:10.1016/j.ibmb.2011.11.007
↑ Mon H, Kobayashi I, Ohkubo S, Tomita S, Lee J, Sezutsu H, Tamura T, Kusakabe T. Effective RNA interference in cultured silkworm cells mediated by overexpression of Caenorhabditis elegans SID-1. RNA Biol. 2012 Jan;9(1):40-6. PMID:22293577 doi:10.4161/rna.9.1.18084
↑ McEwan DL, Weisman AS, Hunter CP. Uptake of extracellular double-stranded RNA by SID-2. Mol Cell. 2012 Sep 14;47(5):746-54. PMID:22902558 doi:10.1016/j.molcel.2012.07.014
↑ Li W, Koutmou KS, Leahy DJ, Li M. Systemic RNA Interference Deficiency-1 (SID-1) Extracellular Domain Selectively Binds Long Double-stranded RNA and Is Required for RNA Transport by SID-1. J Biol Chem. 2015 Jul 31;290(31):18904-13. PMID:26067272 doi:10.1074/jbc.M115.658864
↑ Kaletsky R, Moore RS, Vrla GD, Parsons LR, Gitai Z, Murphy CT. C. elegans interprets bacterial non-coding RNAs to learn pathogenic avoidance. Nature. 2020 Oct;586(7829):445-451. PMID:32908307 doi:10.1038/s41586-020-2699-5

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OCA

[1] Winston WM, Molodowitch C, Hunter CP. Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Science. 2002 Mar 29;295(5564):2456-9. PMID:11834782 doi:10.1126/science.1068836

[2] Feinberg EH, Hunter CP. Transport of dsRNA into cells by the transmembrane protein SID-1. Science. 2003 Sep 12;301(5639):1545-7. PMID:12970568 doi:10.1126/science.1087117

[3] Tijsterman M, May RC, Simmer F, Okihara KL, Plasterk RH. Genes required for systemic RNA interference in Caenorhabditis elegans. Curr Biol. 2004 Jan 20;14(2):111-6. PMID:14738731 doi:10.1016/j.cub.2003.12.029

[4] Hunter CP, Winston WM, Molodowitch C, Feinberg EH, Shih J, Sutherlin M, Wright AJ, Fitzgerald MC. Systemic RNAi in Caenorhabditis elegans. Cold Spring Harb Symp Quant Biol. 2006;71:95-100. PMID:17381285 doi:10.1101/sqb.2006.71.060

[5] Shih JD, Fitzgerald MC, Sutherlin M, Hunter CP. The SID-1 double-stranded RNA transporter is not selective for dsRNA length. RNA. 2009 Mar;15(3):384-90. PMID:19155320 doi:10.1261/rna.1286409

[6] Jose AM, Smith JJ, Hunter CP. Export of RNA silencing from C. elegans tissues does not require the RNA channel SID-1. Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2283-8. PMID:19168628 doi:10.1073/pnas.0809760106

[7] Calixto A, Chelur D, Topalidou I, Chen X, Chalfie M. Enhanced neuronal RNAi in C. elegans using SID-1. Nat Methods. 2010 Jul;7(7):554-9. PMID:20512143 doi:10.1038/nmeth.1463

[8] Shih JD, Hunter CP. SID-1 is a dsRNA-selective dsRNA-gated channel. RNA. 2011 Jun;17(6):1057-65. PMID:21474576 doi:10.1261/rna.2596511

[9] Kobayashi I, Tsukioka H, Kômoto N, Uchino K, Sezutsu H, Tamura T, Kusakabe T, Tomita S. SID-1 protein of Caenorhabditis elegans mediates uptake of dsRNA into Bombyx cells. Insect Biochem Mol Biol. 2012 Feb;42(2):148-54. PMID:22178129 doi:10.1016/j.ibmb.2011.11.007

[10] Mon H, Kobayashi I, Ohkubo S, Tomita S, Lee J, Sezutsu H, Tamura T, Kusakabe T. Effective RNA interference in cultured silkworm cells mediated by overexpression of Caenorhabditis elegans SID-1. RNA Biol. 2012 Jan;9(1):40-6. PMID:22293577 doi:10.4161/rna.9.1.18084

[11] McEwan DL, Weisman AS, Hunter CP. Uptake of extracellular double-stranded RNA by SID-2. Mol Cell. 2012 Sep 14;47(5):746-54. PMID:22902558 doi:10.1016/j.molcel.2012.07.014

[12] Li W, Koutmou KS, Leahy DJ, Li M. Systemic RNA Interference Deficiency-1 (SID-1) Extracellular Domain Selectively Binds Long Double-stranded RNA and Is Required for RNA Transport by SID-1. J Biol Chem. 2015 Jul 31;290(31):18904-13. PMID:26067272 doi:10.1074/jbc.M115.658864

[13] Kaletsky R, Moore RS, Vrla GD, Parsons LR, Gitai Z, Murphy CT. C. elegans interprets bacterial non-coding RNAs to learn pathogenic avoidance. Nature. 2020 Oct;586(7829):445-451. PMID:32908307 doi:10.1038/s41586-020-2699-5

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@@ Line 5: / Line 5: @@
 <table><tr><td colspan='2'>[[9l8m]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9L8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9L8M 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]] 2.9&#8491;</td></tr>
-<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LBN:[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propyl]+2-(trimethylazaniumyl)ethyl+phosphate'>LBN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=Y01:CHOLESTEROL+HEMISUCCINATE'>Y01</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LBN:(2R)-3-(hexadecanoyloxy)-2-{[(9Z)-octadec-9-enoyl]oxy}propyl+2-(trimethylazaniumyl)ethyl+phosphate'>LBN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=Y01:CHOLESTEROL+HEMISUCCINATE'>Y01</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=9l8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9l8m OCA], [https://pdbe.org/9l8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9l8m RCSB], [https://www.ebi.ac.uk/pdbsum/9l8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9l8m ProSAT]</span></td></tr>
 </table>

9l8m: Difference between revisions

Latest revision as of 20:25, 8 September 2026

Structure of SID-1 in complex with dsRNA

Structural highlights

Function

References

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