6rt6
From Proteopedia
(Difference between revisions)
m (Protected "6rt6" [edit=sysop:move=sysop]) |
|||
| (2 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | The | + | ==The YTH domain of YTHDC1 protein in complex with GGm6AC oligonucleotide== |
| + | <StructureSection load='6rt6' size='340' side='right'caption='[[6rt6]], [[Resolution|resolution]] 1.46Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6rt6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RT6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RT6 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]] 1.461Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6rt6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rt6 OCA], [https://pdbe.org/6rt6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rt6 RCSB], [https://www.ebi.ac.uk/pdbsum/6rt6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rt6 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/YTDC1_HUMAN YTDC1_HUMAN] RNA-binding protein that regulates alternative splice site selection.<ref>PMID:20167602</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | N6-methyladenosine (m(6)A) is the most prevalent chemical modification in human mRNAs. Its recognition by reader proteins enables many cellular functions, including splicing and translation of mRNAs. However, the binding mechanisms of m(6)A-containing RNAs to their readers are still elusive due to the unclear roles of m(6)A-flanking ribonucleotides. Here, we use a model system, YTHDC1 with its RNA motif 5'-G-2G-1(m(6)A)C+1U+2-3', to investigate the binding mechanisms by atomistic simulations, X-ray crystallography, and isothermal titration calorimetry. The experimental data and simulation results show that m(6)A is captured by an aromatic cage of YTHDC1 and the 3' terminus nucleotides are stabilized by cation-pi-pi interactions, while the 5' terminus remains flexible. Moreover, simulations of unbound RNA motifs reveal that the methyl group of m(6)A and the 5' terminus shift the conformational preferences of the oligoribonucleotides to the bound-like conformation, thereby facilitating the association process. The binding mechanisms may help in the discovery of chemical probes against m(6)A reader proteins. | ||
| - | + | Flexible binding of m(6)A reader protein YTHDC1 to its preferred RNA motif.,Li Y, Bedi RK, Wiedmer L, Huang D, Sledz P, Caflisch A J Chem Theory Comput. 2019 Oct 31. doi: 10.1021/acs.jctc.9b00987. PMID:31670957<ref>PMID:31670957</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: Bedi | + | <div class="pdbe-citations 6rt6" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: | + | <references/> |
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Homo sapiens]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Bedi R]] | ||
| + | [[Category: Caflisch A]] | ||
| + | [[Category: Sledz P]] | ||
Current revision
The YTH domain of YTHDC1 protein in complex with GGm6AC oligonucleotide
| |||||||||||
