4g0q: Difference between revisions

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 ==Crystal structure of Arabidopsis thaliana AGO1 MID domain in complex with CMP==
-<StructureSection load='4g0q' size='340' side='right' caption='[[4g0q]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='4g0q' size='340' side='right'caption='[[4g0q]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4g0q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G0Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G0Q FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4g0q]] is a 1 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=4G0Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G0Q FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4g0m|4g0m]], [[4g0o|4g0o]], [[4g0p|4g0p]], [[4g0x|4g0x]], [[4g0y|4g0y]], [[4g0z|4g0z]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AGO1, At1g48410, F11A17.3, T1N15.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</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=4g0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g0q OCA], [https://pdbe.org/4g0q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g0q RCSB], [https://www.ebi.ac.uk/pdbsum/4g0q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g0q ProSAT]</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=4g0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g0q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4g0q RCSB], [http://www.ebi.ac.uk/pdbsum/4g0q PDBsum]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/AGO1_ARATH AGO1_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. Requires DRB1 for directional loading of the small RNA duplex (guide stand and passenger strand) onto RISC for passenger strand degradation. Unlike animal RISC that associates in high molecular weight complex, Arabidopsis RISC is probably composed only of the AGO1 protein and associated RNA without any other proteins. Associates mainly with miRNAs of 21 nucleotide in length and preferentially recruits small RNAs with a 5' terminal uridine. Associates with 22 nucleotide miRNAs to trigger RDR6-dependent secondary siRNAs biogenesis. This pathway amplifies silencing by using the target RNA as substrate to generate secondary siRNAs. Binds to miR168 which targets its own mRNA for repression, establishing a homeostatic regulatory loop. Involved in antiviral RNA silencing by contributing to viral RNA clearance. Is capable of targeting viral RNAs with more compact structures than AGO7 which favors less structured RNA targets. May not associate with 24 nucleotide siRNAs involved in chromatin silencing. Essential for multiple processes in development. Essential for proper development of leaves and floral organs, and formation of axillary meristems. Like AGO10, required for stem cell function and organ polarity.<ref>PMID:9427751</ref> <ref>PMID:15882589</ref> <ref>PMID:16081530</ref> <ref>PMID:17158744</ref> <ref>PMID:18342361</ref> <ref>PMID:18342362</ref> <ref>PMID:18344228</ref> <ref>PMID:18799732</ref> <ref>PMID:20562854</ref> <ref>PMID:19763164</ref> <ref>PMID:19861421</ref>
-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<ref>PMID:22850669</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Argonaute|Argonaute]]
+*[[Argonaute 3D structures|Argonaute 3D structures]]
 == References ==
 <references/>
@@ Line 24: / Line 18: @@
 </StructureSection>
 [[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]]