4g0q: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
==Crystal structure of Arabidopsis thaliana AGO1 MID domain in complex with CMP==
==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 ==
== 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><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene><br>
</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><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><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><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>
<table>
== Function ==
<div style="background-color:#fffaf0;">
[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>  
== 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<ref>PMID:22850669</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Argonaute|Argonaute]]
*[[Argonaute 3D structures|Argonaute 3D structures]]
== References ==
== References ==
<references/>
<references/>
Line 24: Line 18:
</StructureSection>
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[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]]

Latest revision as of 14:24, 1 March 2024

Crystal structure of Arabidopsis thaliana AGO1 MID domain in complex with CMPCrystal structure of Arabidopsis thaliana AGO1 MID domain in complex with CMP

Structural highlights

4g0q is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11]

See Also

References

  1. ↑ Bohmert K, Camus I, Bellini C, Bouchez D, Caboche M, Benning C. AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO J. 1998 Jan 2;17(1):170-80. PMID:9427751 doi:http://dx.doi.org/10.1093/emboj/17.1.170
  2. ↑ Kidner CA, Martienssen RA. The role of ARGONAUTE1 (AGO1) in meristem formation and identity. Dev Biol. 2005 Apr 15;280(2):504-17. PMID:15882589 doi:http://dx.doi.org/10.1016/j.ydbio.2005.01.031
  3. ↑ Baumberger N, Baulcombe DC. Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11928-33. Epub 2005 Aug 4. PMID:16081530 doi:http://dx.doi.org/10.1073/pnas.0505461102
  4. ↑ Zhang X, Yuan YR, Pei Y, Lin SS, Tuschl T, Patel DJ, Chua NH. Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev. 2006 Dec 1;20(23):3255-68. PMID:17158744 doi:http://dx.doi.org/20/23/3255
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ Qu F, Ye X, Morris TJ. Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1. Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14732-7. doi:, 10.1073/pnas.0805760105. Epub 2008 Sep 17. PMID:18799732 doi:http://dx.doi.org/10.1073/pnas.0805760105
  9. ↑ Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, Takeda A, Sullivan CM, Gilbert SD, Montgomery TA, Carrington JC. Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nat Struct Mol Biol. 2010 Aug;17(8):997-1003. doi: 10.1038/nsmb.1866. Epub 2010, Jun 18. PMID:20562854 doi:http://dx.doi.org/10.1038/nsmb.1866
  10. ↑ 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
  11. ↑ Eamens AL, Smith NA, Curtin SJ, Wang MB, Waterhouse PM. The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. RNA. 2009 Dec;15(12):2219-35. doi: 10.1261/rna.1646909. Epub 2009 Oct 27. PMID:19861421 doi:http://dx.doi.org/10.1261/rna.1646909

4g0q, resolution 1.80Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=4g0q&oldid=4073674"