6sz8
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of YTHDC1 with fragment 6 (DHU_DC1_034)== | |
| + | <StructureSection load='6sz8' size='340' side='right'caption='[[6sz8]], [[Resolution|resolution]] 1.47Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6sz8]] is a 2 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=6SZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SZ8 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]] 1.47Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M1Z:6-pyrrolidin-1-yl-5~{H}-pyrimidine-2,4-dione'>M1Z</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=6sz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sz8 OCA], [https://pdbe.org/6sz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sz8 RCSB], [https://www.ebi.ac.uk/pdbsum/6sz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sz8 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/A0A2K6KCS5_RHIBE A0A2K6KCS5_RHIBE] Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs, and regulates mRNA stability. M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in mRNA stability and processing.[RuleBase:RU369095] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | We report a crystallographic analysis of small-molecule ligands of the human YTHDC1 domain that recognizes N6-methylated adenine (m(6)A) in RNA. The 30 binders are fragments (molecular weight < 300 g mol(-1)) that represent 10 different chemotypes identified by virtual screening. Despite the structural disorder of the binding site loop (residues 429-439), most of the 30 fragments emulate the two main interactions of the -NHCH3 group of m(6)A. These interactions are the hydrogen bond to the backbone carbonyl of Ser378 and the van der Waals contacts with the tryptophan cage. Different chemical groups are involved in the conserved binding motifs. Some of the fragments show favorable ligand efficiency for YTHDC1 and selectivity against other m(6)A reader domains. The structural information is useful for the design of modulators of m(6)A recognition by YTHDC1. | ||
| - | + | Selectively Disrupting m(6)A-Dependent Protein-RNA Interactions with Fragments.,Bedi RK, Huang D, Wiedmer L, Li Y, Dolbois A, Wojdyla JA, Sharpe ME, Caflisch A, Sledz P ACS Chem Biol. 2020 Mar 2. doi: 10.1021/acschembio.9b00894. PMID:32101404<ref>PMID:32101404</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 6sz8" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: | + | <references/> |
| - | [[Category: Huang | + | __TOC__ |
| + | </StructureSection> | ||
| + | [[Category: Homo sapiens]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Bedi RK]] | ||
| + | [[Category: Caflisch A]] | ||
| + | [[Category: Huang D]] | ||
| + | [[Category: Sledz P]] | ||
Current revision
Crystal structure of YTHDC1 with fragment 6 (DHU_DC1_034)
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