4g0m

From Proteopedia

(Difference between revisions)

Revision as of 20:18, 19 October 2022

Crystal structure of Arabidopsis thaliana AGO2 MID domain

Structural highlights

4g0m is a 2 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AGO2_ARATH Involved in RNA-mediated post-transcriptional gene silencing (PTGS). Main component of the RNA-induced silencing complex (RISC) that binds to a short guide RNA such as microRNA (miRNA) or small interfering RNA (siRNA). RISC uses the mature miRNA or siRNA as a guide for slicer-directed cleavage of homologous mRNAs to repress gene expression. Associates mainly with siRNAs of 21 nucleotide in length and preferentially recruits small RNAs with a 5' terminal adenosine. Probably involved in antiviral RNA silencing. Associates with siRNA derived from cucumber mosaic virus (CMV). Targeted by turnip yellows virus (TuYV) protein P0 (via F-box-like domain) for probable proteasome degradation and thereby inactivating AGO2 function in RNA silencing. Required to direct NERD-dependent DNA methylation and silencing.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

The 5'-nucleotide of small RNAs associates directly with the MID domain of Argonaute (AGO) proteins. In humans, the identity of the 5'-base is sensed by the MID domain nucleotide specificity loop and regulates the integrity of miRNAs. In Arabidopsis thaliana, the 5'-nucleotide also controls sorting of small RNAs into the appropriate member of the AGO family; however, the structural basis for this mechanism is unknown. Here, we present crystal structures of the MID domain from three Arabidopsis AGOs, AtAGO1, AtAGO2 and AtAGO5, and characterize their interactions with nucleoside monophosphates (NMPs). In AtAGOs, the nucleotide specificity loop also senses the identity of the 5'-nucleotide but uses more diverse modes of recognition owing to the greater complexity of small RNAs found in plants. Binding analyses of these interactions reveal a strong correlation between their affinities and evolutionary conservation.

Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs.,Frank F, Hauver J, Sonenberg N, Nagar B EMBO J. 2012 Jul 31. doi: 10.1038/emboj.2012.204. PMID:22850669^[6]

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

References

↑ Baumberger N, Tsai CH, Lie M, Havecker E, Baulcombe DC. The Polerovirus silencing suppressor P0 targets ARGONAUTE proteins for degradation. Curr Biol. 2007 Sep 18;17(18):1609-14. PMID:17869110 doi:http://dx.doi.org/10.1016/j.cub.2007.08.039
↑ Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, Chen S, Hannon GJ, Qi Y. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell. 2008 Apr 4;133(1):116-27. doi: 10.1016/j.cell.2008.02.034. Epub 2008 Mar, 13. PMID:18342361 doi:http://dx.doi.org/10.1016/j.cell.2008.02.034
↑ Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell. 2008 Apr 4;133(1):128-41. doi: 10.1016/j.cell.2008.02.033. Epub 2008 Mar, 13. PMID:18342362 doi:http://dx.doi.org/10.1016/j.cell.2008.02.033
↑ Takeda A, Iwasaki S, Watanabe T, Utsumi M, Watanabe Y. The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins. Plant Cell Physiol. 2008 Apr;49(4):493-500. doi: 10.1093/pcp/pcn043. Epub 2008, Mar 14. PMID:18344228 doi:http://dx.doi.org/10.1093/pcp/pcn043
↑ Pontier D, Picart C, Roudier F, Garcia D, Lahmy S, Azevedo J, Alart E, Laudie M, Karlowski WM, Cooke R, Colot V, Voinnet O, Lagrange T. NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis. Mol Cell. 2012 Oct 12;48(1):121-32. doi: 10.1016/j.molcel.2012.07.027. Epub 2012 , Aug 30. PMID:22940247 doi:http://dx.doi.org/10.1016/j.molcel.2012.07.027
↑ Frank F, Hauver J, Sonenberg N, Nagar B. Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs. EMBO J. 2012 Jul 31. doi: 10.1038/emboj.2012.204. PMID:22850669 doi:10.1038/emboj.2012.204

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/4g0m"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Arabidopsis thaliana AGO2 MID domain==
-<StructureSection load='4g0m' size='340' side='right' caption='[[4g0m]], [[Resolution|resolution]] 2.31&Aring;' scene=''>
+<StructureSection load='4g0m' size='340' side='right'caption='[[4g0m]], [[Resolution|resolution]] 2.31&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4g0m]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G0M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4g0m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G0M FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4g0o|4g0o]], [[4g0p|4g0p]], [[4g0q|4g0q]], [[4g0x|4g0x]], [[4g0y|4g0y]], [[4g0z|4g0z]]</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=4g0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g0m OCA], [https://pdbe.org/4g0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g0m RCSB], [https://www.ebi.ac.uk/pdbsum/4g0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g0m ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AGO2, At1g31280, T19E23.7T19E23_8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=4g0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g0m OCA], [http://pdbe.org/4g0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4g0m RCSB], [http://www.ebi.ac.uk/pdbsum/4g0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4g0m ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/AGO2_ARATH AGO2_ARATH]] Involved in RNA-mediated post-transcriptional gene silencing (PTGS). Main component of the RNA-induced silencing complex (RISC) that binds to a short guide RNA such as microRNA (miRNA) or small interfering RNA (siRNA). RISC uses the mature miRNA or siRNA as a guide for slicer-directed cleavage of homologous mRNAs to repress gene expression. Associates mainly with siRNAs of 21 nucleotide in length and preferentially recruits small RNAs with a 5' terminal adenosine. Probably involved in antiviral RNA silencing. Associates with siRNA derived from cucumber mosaic virus (CMV). Targeted by turnip yellows virus (TuYV) protein P0 (via F-box-like domain) for probable proteasome degradation and thereby inactivating AGO2 function in RNA silencing. Required to direct NERD-dependent DNA methylation and silencing.<ref>PMID:17869110</ref> <ref>PMID:18342361</ref> <ref>PMID:18342362</ref> <ref>PMID:18344228</ref> <ref>PMID:22940247</ref>
+[https://www.uniprot.org/uniprot/AGO2_ARATH AGO2_ARATH] Involved in RNA-mediated post-transcriptional gene silencing (PTGS). Main component of the RNA-induced silencing complex (RISC) that binds to a short guide RNA such as microRNA (miRNA) or small interfering RNA (siRNA). RISC uses the mature miRNA or siRNA as a guide for slicer-directed cleavage of homologous mRNAs to repress gene expression. Associates mainly with siRNAs of 21 nucleotide in length and preferentially recruits small RNAs with a 5' terminal adenosine. Probably involved in antiviral RNA silencing. Associates with siRNA derived from cucumber mosaic virus (CMV). Targeted by turnip yellows virus (TuYV) protein P0 (via F-box-like domain) for probable proteasome degradation and thereby inactivating AGO2 function in RNA silencing. Required to direct NERD-dependent DNA methylation and silencing.<ref>PMID:17869110</ref> <ref>PMID:18342361</ref> <ref>PMID:18342362</ref> <ref>PMID:18344228</ref> <ref>PMID:22940247</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 20: @@
 ==See Also==
-*[[Argonaute|Argonaute]]
+*[[Argonaute 3D structures|Argonaute 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Frank, F]]
+[[Category: Large Structures]]
-[[Category: Hauver, J]]
+[[Category: Frank F]]
-[[Category: Nagar, B]]
+[[Category: Hauver J]]
-[[Category: Sonenberg, N]]
+[[Category: Nagar B]]
-[[Category: Gene regulation]]
+[[Category: Sonenberg N]]
-[[Category: Mid domain]]
-[[Category: Small rna 5' nucleotide recognition]]

4g0m

From Proteopedia

Revision as of 20:18, 19 October 2022

Crystal structure of Arabidopsis thaliana AGO2 MID domain

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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