5gio: Difference between revisions
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New page: '''Unreleased structure''' The entry 5gio is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures |
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==Crystal structure of box C/D RNP with 12 nt guide regions and 13 nt substrates== | |||
<StructureSection load='5gio' size='340' side='right'caption='[[5gio]], [[Resolution|resolution]] 3.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5gio]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GIO FirstGlance]. <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]] 3.604Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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=5gio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gio OCA], [https://pdbe.org/5gio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gio RCSB], [https://www.ebi.ac.uk/pdbsum/5gio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gio ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q97ZH3_SACS2 Q97ZH3_SACS2] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Box C/D RNAs guide site-specific 2'-O-methylation of RNAs in archaea and eukaryotes. The spacer regions between boxes C to D' and boxes C' to D contain the guide sequence that can form a stretch of base pairs with substrate RNAs. The lengths of spacer regions and guide-substrate duplexes are variable among C/D RNAs. In a previously determined structure of C/D ribonucleoprotein (RNP), a 12-nt-long spacer forms 10 bp with the substrate. How spacers and guide-substrate duplexes of other lengths are accommodated remains unknown. Here we analyze how the lengths of spacers and guide-substrate duplexes affect the modification activity and determine three structures of C/D RNPs assembled with different spacers and substrates. We show that the guide can only form a duplex of a maximum of 10 bp with the substrate during modification. Slightly shorter duplexes are tolerated, but longer duplexes must be unwound to fit into a capped protein channel for modification. Spacers with <12 nucleotides are defective, mainly because they cannot load the substrate in the active conformation. For spacers with >12 nucleotides, the excessive unpaired sequences near the box C/C' side are looped out. Our results provide insight into the substrate recognition mechanism of C/D RNA and refute the RNA-swapped model for dimeric C/D RNP. | |||
Box C/D guide RNAs recognize a maximum of 10 nt of substrates.,Yang Z, Lin J, Ye K Proc Natl Acad Sci U S A. 2016 Sep 27;113(39):10878-83. doi:, 10.1073/pnas.1604872113. Epub 2016 Sep 13. PMID:27625427<ref>PMID:27625427</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 5gio" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Saccharolobus solfataricus]] | |||
[[Category: Lin J]] | |||
[[Category: Yang Z]] | |||
[[Category: Ye K]] | |||
Latest revision as of 11:32, 2 August 2023
Crystal structure of box C/D RNP with 12 nt guide regions and 13 nt substrates
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