7swf: Difference between revisions

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'''Unreleased structure'''


The entry 7swf is ON HOLD  until Paper Publication
==Cryo-EM structure of Arabidopsis Ago10-guide-target RNA complex in a central duplex conformation==
<StructureSection load='7swf' size='340' side='right'caption='[[7swf]], [[Resolution|resolution]] 3.79&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7swf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7SWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SWF 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]] 3.79&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7swf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7swf OCA], [https://pdbe.org/7swf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7swf RCSB], [https://www.ebi.ac.uk/pdbsum/7swf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7swf ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/AGO10_ARATH AGO10_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 a 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. Required for reliable formation of primary and axillary shoot apical meristems. Specifies leaf adaxial identity by repressing the miR165 and miR166 microRNAs in the embryonic shoot apex, in the shoot apical meristem (SAM) and leaf. Represses the microRNA miR398 which targets CCS1 chaperone mRNAs for translational inhibition. Acts as a negative regulator of AGO1 protein level. Like AGO1, is required for stem cell function and organ polarity. Unlike AGO1, is not subjected to small RNA-mediated repression itself. Essential for multiple processes in development. Coregulates, with GATA18/HAN, the shoot apical meristem (SAM) organization (PubMed:26390296).<ref>PMID:12468725</ref> <ref>PMID:19054365</ref> <ref>PMID:19763164</ref> <ref>PMID:20128885</ref> <ref>PMID:26390296</ref> <ref>PMID:9501101</ref> <ref>PMID:9876176</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Small RNAs (sRNAs), including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are essential gene regulators for plant and animal development. The loading of sRNA duplexes into the proper ARGONAUTE (AGO) protein is a key step to forming a functional silencing complex. In Arabidopsis thaliana, the specific loading of miR166/165 into AGO10 (AtAGO10) is critical for the maintenance of the shoot apical meristem, the source of all shoot organs, but the mechanism by which AtAGO10 distinguishes miR166/165 from other cellular miRNAs is not known. Here, we show purified AtAGO10 alone lacks loading selectivity towards miR166/165 duplexes. However, phosphate and HSP chaperone systems reshape the selectivity of AtAGO10 to its physiological substrates. A loop in the AtAGO10 central cleft is essential for recognizing specific mismatches opposite the guide strand 3' region in miR166/165 duplexes. Replacing this loop with the equivalent loop from Homo sapiens AGO2 (HsAGO2) changes AtAGO10 miRNA loading behavior such that 3' region mismatches are ignored and mismatches opposite the guide 5' end instead drive loading, as in HsAGO2. Thus, this study uncovers the molecular mechanism underlying the miR166/165 selectivity of AtAGO10, essential for plant development, and provides new insights into how miRNA duplex structures are recognized for sRNA sorting.


Authors:  
The molecular mechanism of microRNA duplex selectivity of Arabidopsis ARGONAUTE10.,Xiao Y, MacRae IJ Nucleic Acids Res. 2022 Sep 23;50(17):10041-10052. doi: 10.1093/nar/gkac571. PMID:35801914<ref>PMID:35801914</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 7swf" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Argonaute 3D structures|Argonaute 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Large Structures]]
[[Category: Unidentified]]
[[Category: MacRae IJ]]
[[Category: Xiao Y]]

Latest revision as of 08:53, 5 June 2024

Cryo-EM structure of Arabidopsis Ago10-guide-target RNA complex in a central duplex conformationCryo-EM structure of Arabidopsis Ago10-guide-target RNA complex in a central duplex conformation

Structural highlights

7swf is a 3 chain structure with sequence from Arabidopsis thaliana and Unidentified. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Electron Microscopy, Resolution 3.79Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AGO10_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 a 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. Required for reliable formation of primary and axillary shoot apical meristems. Specifies leaf adaxial identity by repressing the miR165 and miR166 microRNAs in the embryonic shoot apex, in the shoot apical meristem (SAM) and leaf. Represses the microRNA miR398 which targets CCS1 chaperone mRNAs for translational inhibition. Acts as a negative regulator of AGO1 protein level. Like AGO1, is required for stem cell function and organ polarity. Unlike AGO1, is not subjected to small RNA-mediated repression itself. Essential for multiple processes in development. Coregulates, with GATA18/HAN, the shoot apical meristem (SAM) organization (PubMed:26390296).[1] [2] [3] [4] [5] [6] [7]

Publication Abstract from PubMed

Small RNAs (sRNAs), including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are essential gene regulators for plant and animal development. The loading of sRNA duplexes into the proper ARGONAUTE (AGO) protein is a key step to forming a functional silencing complex. In Arabidopsis thaliana, the specific loading of miR166/165 into AGO10 (AtAGO10) is critical for the maintenance of the shoot apical meristem, the source of all shoot organs, but the mechanism by which AtAGO10 distinguishes miR166/165 from other cellular miRNAs is not known. Here, we show purified AtAGO10 alone lacks loading selectivity towards miR166/165 duplexes. However, phosphate and HSP chaperone systems reshape the selectivity of AtAGO10 to its physiological substrates. A loop in the AtAGO10 central cleft is essential for recognizing specific mismatches opposite the guide strand 3' region in miR166/165 duplexes. Replacing this loop with the equivalent loop from Homo sapiens AGO2 (HsAGO2) changes AtAGO10 miRNA loading behavior such that 3' region mismatches are ignored and mismatches opposite the guide 5' end instead drive loading, as in HsAGO2. Thus, this study uncovers the molecular mechanism underlying the miR166/165 selectivity of AtAGO10, essential for plant development, and provides new insights into how miRNA duplex structures are recognized for sRNA sorting.

The molecular mechanism of microRNA duplex selectivity of Arabidopsis ARGONAUTE10.,Xiao Y, MacRae IJ Nucleic Acids Res. 2022 Sep 23;50(17):10041-10052. doi: 10.1093/nar/gkac571. PMID:35801914[8]

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

See Also

References

  1. ↑ Newman KL, Fernandez AG, Barton MK. Regulation of axis determinacy by the Arabidopsis PINHEAD gene. Plant Cell. 2002 Dec;14(12):3029-42. doi: 10.1105/tpc.005132. PMID:12468725 doi:http://dx.doi.org/10.1105/tpc.005132
  2. ↑ Liu Q, Yao X, Pi L, Wang H, Cui X, Huang H. The ARGONAUTE10 gene modulates shoot apical meristem maintenance and establishment of leaf polarity by repressing miR165/166 in Arabidopsis. Plant J. 2009 Apr;58(1):27-40. doi: 10.1111/j.1365-313X.2008.03757.x. Epub 2008, Dec 29. PMID:19054365 doi:http://dx.doi.org/10.1111/j.1365-313X.2008.03757.x
  3. ↑ Mallory AC, Hinze A, Tucker MR, Bouche N, Gasciolli V, Elmayan T, Lauressergues D, Jauvion V, Vaucheret H, Laux T. Redundant and specific roles of the ARGONAUTE proteins AGO1 and ZLL in development and small RNA-directed gene silencing. PLoS Genet. 2009 Sep;5(9):e1000646. doi: 10.1371/journal.pgen.1000646. Epub 2009 , Sep 18. PMID:19763164 doi:http://dx.doi.org/10.1371/journal.pgen.1000646
  4. ↑ Beauclair L, Yu A, Bouche N. microRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis. Plant J. 2010 May;62(3):454-62. doi: 10.1111/j.1365-313X.2010.04162.x. Epub 2010 , Feb 1. PMID:20128885 doi:http://dx.doi.org/10.1111/j.1365-313X.2010.04162.x
  5. ↑ Ding L, Yan S, Jiang L, Zhao W, Ning K, Zhao J, Liu X, Zhang J, Wang Q, Zhang X. HANABA TARANU (HAN) Bridges Meristem and Organ Primordia Boundaries through PINHEAD, JAGGED, BLADE-ON-PETIOLE2 and CYTOKININ OXIDASE 3 during Flower Development in Arabidopsis. PLoS Genet. 2015 Sep 21;11(9):e1005479. doi: 10.1371/journal.pgen.1005479., eCollection 2015 Sep. PMID:26390296 doi:http://dx.doi.org/10.1371/journal.pgen.1005479
  6. ↑ Moussian B, Schoof H, Haecker A, Jurgens G, Laux T. Role of the ZWILLE gene in the regulation of central shoot meristem cell fate during Arabidopsis embryogenesis. EMBO J. 1998 Mar 16;17(6):1799-809. doi: 10.1093/emboj/17.6.1799. PMID:9501101 doi:http://dx.doi.org/10.1093/emboj/17.6.1799
  7. ↑ Lynn K, Fernandez A, Aida M, Sedbrook J, Tasaka M, Masson P, Barton MK. The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene. Development. 1999 Feb;126(3):469-81. PMID:9876176
  8. ↑ Xiao Y, MacRae IJ. The molecular mechanism of microRNA duplex selectivity of Arabidopsis ARGONAUTE10. Nucleic Acids Res. 2022 Jul 8. pii: 6633885. doi: 10.1093/nar/gkac571. PMID:35801914 doi:http://dx.doi.org/10.1093/nar/gkac571

7swf, resolution 3.79Å

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