|
|
| Line 3: |
Line 3: |
| | <StructureSection load='6rt4' size='340' side='right'caption='[[6rt4]], [[Resolution|resolution]] 1.49Å' scene=''> | | <StructureSection load='6rt4' size='340' side='right'caption='[[6rt4]], [[Resolution|resolution]] 1.49Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6rt4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RT4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RT4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6rt4]] 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=6RT4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RT4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.49Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YTHDC1, KIAA1966, YT521 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6rt4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rt4 OCA], [https://pdbe.org/6rt4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rt4 RCSB], [https://www.ebi.ac.uk/pdbsum/6rt4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rt4 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6rt4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rt4 OCA], [http://pdbe.org/6rt4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rt4 RCSB], [http://www.ebi.ac.uk/pdbsum/6rt4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rt4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/YTDC1_HUMAN YTDC1_HUMAN]] RNA-binding protein that regulates alternative splice site selection.<ref>PMID:20167602</ref> | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 24: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bedi, R]] | + | [[Category: Bedi R]] |
| - | [[Category: Caflisch, A]] | + | [[Category: Caflisch A]] |
| - | [[Category: Sledz, P]] | + | [[Category: Sledz P]] |
| - | [[Category: Epitranscriptomic]]
| + | |
| - | [[Category: Protein-rna interaction]]
| + | |
| - | [[Category: Rna binding protein]]
| + | |
| Structural highlights
Function
YTDC1_HUMAN RNA-binding protein that regulates alternative splice site selection.[1]
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Zhang Z, Theler D, Kaminska KH, Hiller M, de la Grange P, Pudimat R, Rafalska I, Heinrich B, Bujnicki JM, Allain FH, Stamm S. The YTH domain is a novel RNA binding domain. J Biol Chem. 2010 May 7;285(19):14701-10. doi: 10.1074/jbc.M110.104711. Epub 2010, Feb 18. PMID:20167602 doi:http://dx.doi.org/10.1074/jbc.M110.104711
- ↑ Li Y, Bedi RK, Wiedmer L, Huang D, Sledz P, Caflisch A. Flexible binding of m(6)A reader protein YTHDC1 to its preferred RNA motif. J Chem Theory Comput. 2019 Oct 31. doi: 10.1021/acs.jctc.9b00987. PMID:31670957 doi:http://dx.doi.org/10.1021/acs.jctc.9b00987
|
