5js2

From Proteopedia

(Difference between revisions)

Revision as of 11:35, 17 June 2020

Human Argonaute-2 Bound to a Modified siRNA

Structural highlights

5js2 is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
NonStd Res:	, , , ,
Related:	5js1
Gene:	AGO2, EIF2C2 (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[AGO2_HUMAN] Required for RNA-mediated gene silencing (RNAi) by the RNA-induced silencing complex (RISC). The 'minimal RISC' appears to include EIF2C2/AGO2 bound to a short guide RNA such as a microRNA (miRNA) or short interfering RNA (siRNA). These guide RNAs direct RISC to complementary mRNAs that are targets for RISC-mediated gene silencing. The precise mechanism of gene silencing depends on the degree of complementarity between the miRNA or siRNA and its target. Binding of RISC to a perfectly complementary mRNA generally results in silencing due to endonucleolytic cleavage of the mRNA specifically by EIF2C2/AGO2. Binding of RISC to a partially complementary mRNA results in silencing through inhibition of translation, and this is independent of endonuclease activity. May inhibit translation initiation by binding to the 7-methylguanosine cap, thereby preventing the recruitment of the translation initiation factor eIF4-E. May also inhibit translation initiation via interaction with EIF6, which itself binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit. The inhibition of translational initiation leads to the accumulation of the affected mRNA in cytoplasmic processing bodies (P-bodies), where mRNA degradation may subsequently occur. In some cases RISC-mediated translational repression is also observed for miRNAs that perfectly match the 3' untranslated region (3'-UTR). Can also up-regulate the translation of specific mRNAs under certain growth conditions. Binds to the AU element of the 3'-UTR of the TNF (TNF-alpha) mRNA and up-regulates translation under conditions of serum starvation. Also required for transcriptional gene silencing (TGS), in which short RNAs known as antigene RNAs or agRNAs direct the transcriptional repression of complementary promoter regions.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17] ^[18] ^[19] ^[20] ^[21] ^[22]

Publication Abstract from PubMed

Incorporation of chemical modifications into small interfering RNAs (siRNAs) increases their metabolic stability and improves their tissue distribution. However, how these modifications impact interactions with Argonaute-2 (Ago2), the molecular target of siRNAs, is not known. Herein we present the crystal structure of human Ago2 bound to a metabolically stable siRNA containing extensive backbone modifications. Comparison to the structure of an equivalent unmodified-siRNA complex indicates that the structure of Ago2 is relatively unaffected by chemical modifications in the bound siRNA. In contrast, the modified siRNA appears to be much more plastic and shifts, relative to the unmodified siRNA, to optimize contacts with Ago2. Structure-activity analysis reveals that even major conformational perturbations in the 3' half of the siRNA seed region have a relatively modest effect on knockdown potency. These findings provide an explanation for a variety of modification patterns tolerated in siRNAs and a structural basis for advancing therapeutic siRNA design.

Structural Analysis of Human Argonaute-2 Bound to a Modified siRNA Guide.,Schirle NT, Kinberger GA, Murray HF, Lima WF, Prakash TP, MacRae IJ J Am Chem Soc. 2016 Jul 20;138(28):8694-7. doi: 10.1021/jacs.6b04454. Epub 2016, Jul 12. PMID:27380263^[23]

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

References

↑ Martinez J, Tuschl T. RISC is a 5' phosphomonoester-producing RNA endonuclease. Genes Dev. 2004 May 1;18(9):975-80. Epub 2004 Apr 22. PMID:15105377 doi:http://dx.doi.org/10.1101/gad.1187904
↑ Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G, Tuschl T. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell. 2004 Jul 23;15(2):185-97. PMID:15260970 doi:http://dx.doi.org/10.1016/j.molcel.2004.07.007
↑ Pillai RS, Artus CG, Filipowicz W. Tethering of human Ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis. RNA. 2004 Oct;10(10):1518-25. Epub 2004 Aug 30. PMID:15337849 doi:http://dx.doi.org/10.1261/rna.7131604
↑ Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua-Tor L, Hannon GJ. Argonaute2 is the catalytic engine of mammalian RNAi. Science. 2004 Sep 3;305(5689):1437-41. Epub 2004 Jul 29. PMID:15284456 doi:http://dx.doi.org/10.1126/science.1102513
↑ Gregory RI, Chendrimada TP, Cooch N, Shiekhattar R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell. 2005 Nov 18;123(4):631-40. Epub 2005 Nov 3. PMID:16271387 doi:10.1016/j.cell.2005.10.022
↑ Meister G, Landthaler M, Peters L, Chen PY, Urlaub H, Luhrmann R, Tuschl T. Identification of novel argonaute-associated proteins. Curr Biol. 2005 Dec 6;15(23):2149-55. Epub 2005 Nov 10. PMID:16289642 doi:10.1016/j.cub.2005.10.048
↑ Haase AD, Jaskiewicz L, Zhang H, Laine S, Sack R, Gatignol A, Filipowicz W. TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep. 2005 Oct;6(10):961-7. PMID:16142218 doi:10.1038/sj.embor.7400509
↑ Maniataki E, Mourelatos Z. A human, ATP-independent, RISC assembly machine fueled by pre-miRNA. Genes Dev. 2005 Dec 15;19(24):2979-90. PMID:16357216 doi:10.1101/gad.1384005
↑ Rivas FV, Tolia NH, Song JJ, Aragon JP, Liu J, Hannon GJ, Joshua-Tor L. Purified Argonaute2 and an siRNA form recombinant human RISC. Nat Struct Mol Biol. 2005 Apr;12(4):340-9. Epub 2005 Mar 30. PMID:15800637 doi:10.1038/nsmb918
↑ Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, Basyuk E, Bertrand E, Filipowicz W. Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science. 2005 Sep 2;309(5740):1573-6. Epub 2005 Aug 4. PMID:16081698 doi:http://dx.doi.org/10.1126/science.1115079
↑ Janowski BA, Huffman KE, Schwartz JC, Ram R, Nordsell R, Shames DS, Minna JD, Corey DR. Involvement of AGO1 and AGO2 in mammalian transcriptional silencing. Nat Struct Mol Biol. 2006 Sep;13(9):787-92. Epub 2006 Aug 27. PMID:16936728 doi:nsmb1140
↑ Chu CY, Rana TM. Translation repression in human cells by microRNA-induced gene silencing requires RCK/p54. PLoS Biol. 2006 Jul;4(7):e210. PMID:16756390 doi:http://dx.doi.org/06-PLBI-RA-0036R3
↑ Vasudevan S, Steitz JA. AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2. Cell. 2007 Mar 23;128(6):1105-18. PMID:17382880 doi:http://dx.doi.org/10.1016/j.cell.2007.01.038
↑ Kiriakidou M, Tan GS, Lamprinaki S, De Planell-Saguer M, Nelson PT, Mourelatos Z. An mRNA m7G cap binding-like motif within human Ago2 represses translation. Cell. 2007 Jun 15;129(6):1141-51. Epub 2007 May 24. PMID:17524464 doi:http://dx.doi.org/10.1016/j.cell.2007.05.016
↑ Hock J, Weinmann L, Ender C, Rudel S, Kremmer E, Raabe M, Urlaub H, Meister G. Proteomic and functional analysis of Argonaute-containing mRNA-protein complexes in human cells. EMBO Rep. 2007 Nov;8(11):1052-60. Epub 2007 Oct 12. PMID:17932509 doi:http://dx.doi.org/7401088
↑ Robb GB, Rana TM. RNA helicase A interacts with RISC in human cells and functions in RISC loading. Mol Cell. 2007 May 25;26(4):523-37. PMID:17531811 doi:http://dx.doi.org/10.1016/j.molcel.2007.04.016
↑ Chendrimada TP, Finn KJ, Ji X, Baillat D, Gregory RI, Liebhaber SA, Pasquinelli AE, Shiekhattar R. MicroRNA silencing through RISC recruitment of eIF6. Nature. 2007 Jun 14;447(7146):823-8. Epub 2007 May 16. PMID:17507929 doi:http://dx.doi.org/10.1038/nature05841
↑ Vasudevan S, Tong Y, Steitz JA. Switching from repression to activation: microRNAs can up-regulate translation. Science. 2007 Dec 21;318(5858):1931-4. Epub 2007 Nov 29. PMID:18048652 doi:http://dx.doi.org/10.1126/science.1149460
↑ Wu L, Fan J, Belasco JG. Importance of translation and nonnucleolytic ago proteins for on-target RNA interference. Curr Biol. 2008 Sep 9;18(17):1327-32. doi: 10.1016/j.cub.2008.07.072. PMID:18771919 doi:10.1016/j.cub.2008.07.072
↑ Qi HH, Ongusaha PP, Myllyharju J, Cheng D, Pakkanen O, Shi Y, Lee SW, Peng J, Shi Y. Prolyl 4-hydroxylation regulates Argonaute 2 stability. Nature. 2008 Sep 18;455(7211):421-4. doi: 10.1038/nature07186. Epub 2008 Aug 6. PMID:18690212 doi:http://dx.doi.org/10.1038/nature07186
↑ MacRae IJ, Ma E, Zhou M, Robinson CV, Doudna JA. In vitro reconstitution of the human RISC-loading complex. Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):512-7. doi: 10.1073/pnas.0710869105., Epub 2008 Jan 4. PMID:18178619 doi:10.1073/pnas.0710869105
↑ Weinmann L, Hock J, Ivacevic T, Ohrt T, Mutze J, Schwille P, Kremmer E, Benes V, Urlaub H, Meister G. Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs. Cell. 2009 Feb 6;136(3):496-507. doi: 10.1016/j.cell.2008.12.023. Epub 2009 Jan, 22. PMID:19167051 doi:http://dx.doi.org/10.1016/j.cell.2008.12.023
↑ Schirle NT, Kinberger GA, Murray HF, Lima WF, Prakash TP, MacRae IJ. Structural Analysis of Human Argonaute-2 Bound to a Modified siRNA Guide. J Am Chem Soc. 2016 Jul 20;138(28):8694-7. doi: 10.1021/jacs.6b04454. Epub 2016, Jul 12. PMID:27380263 doi:http://dx.doi.org/10.1021/jacs.6b04454

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5js2"

@@ Line 1: / Line 1: @@
 ==Human Argonaute-2 Bound to a Modified siRNA==
-<StructureSection load='5js2' size='340' side='right' caption='[[5js2]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
+<StructureSection load='5js2' size='340' side='right'caption='[[5js2]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5js2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JS2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JS2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5js2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JS2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JS2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPH:PHENOL'>IPH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPH:PHENOL'>IPH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6NW:2-O-METHYL-5-O-THIOPHOSPHONOADENOSINE'>6NW</scene>, <scene name='pdbligand=6OO:2-O-METHYL-5-O-THIOPHOSPHONOCYTIDINE'>6OO</scene>, <scene name='pdbligand=6OP:1-[(5E)-5,6-DIDEOXY-2-O-(2-METHOXYETHYL)-6-PHOSPHONO-BETA-D-RIBO-HEX-5-ENOFURANOSYL]-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE'>6OP</scene>, <scene name='pdbligand=F2T:2-DEOXY-2-FLUORO-5-O-THIOPHOSPHONOURIDINE'>F2T</scene>, <scene name='pdbligand=UFT:2-DEOXY-2-FLUOROURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UFT</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5js1|5js1]]</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=5js2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5js2 OCA], [http://pdbe.org/5js2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5js2 RCSB], [http://www.ebi.ac.uk/pdbsum/5js2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5js2 ProSAT]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AGO2, EIF2C2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5js2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5js2 OCA], [http://pdbe.org/5js2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5js2 RCSB], [http://www.ebi.ac.uk/pdbsum/5js2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5js2 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 20: / Line 21: @@
 </div>
 <div class="pdbe-citations 5js2" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Argonaute 3D structures|Argonaute 3D structures]]
+*[[Eukaryotic initiation factor 3D structures|Eukaryotic initiation factor 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: MacRae, I J]]
 [[Category: Schirle, N T]]

5js2

From Proteopedia

Revision as of 11:35, 17 June 2020

Human Argonaute-2 Bound to a Modified siRNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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