6zcn - Revision history

OCA at 13:46, 24 January 2024

OCA — Wed, 24 Jan 2024 13:46:38 GMT

←Older revision		Revision as of 13:46, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6zcn' size='340' side='right'caption='[[6zcn]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6zcn' size='340' side='right'caption='[[6zcn]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6zcn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZCN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZCN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zcn]] 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=6ZCN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZCN FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.6Å</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=6zcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zcn OCA], [https://pdbe.org/6zcn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zcn RCSB], [https://www.ebi.ac.uk/pdbsum/6zcn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zcn ProSAT]</span></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=6zcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zcn OCA], [https://pdbe.org/6zcn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zcn RCSB], [https://www.ebi.ac.uk/pdbsum/6zcn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zcn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://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 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bedi~~, R K~~]]	+	[[Category: Bedi RK]]
-	[[Category: Caflisch, A]]	+	[[Category: Caflisch A]]
-	[[Category: Huang, D]]	+	[[Category: Huang D]]
-	[[Category: Wiedmer, L]]	+	[[Category: Wiedmer L]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: M6a]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Ythdc1~~]]	+

OCA at 10:45, 31 March 2021

OCA — Wed, 31 Mar 2021 10:45:18 GMT

←Older revision		Revision as of 10:45, 31 March 2021
Line 3:		Line 3:
	<StructureSection load='6zcn' size='340' side='right'caption='[[6zcn]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6zcn' size='340' side='right'caption='[[6zcn]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6zcn]] is a 2 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=6ZCN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6ZCN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zcn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZCN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZCN FirstGlance]. <br>
	</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>		</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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6zcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zcn OCA], [~~http~~://pdbe.org/6zcn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6zcn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6zcn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6zcn ProSAT]</span></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=6zcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zcn OCA], [https://pdbe.org/6zcn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zcn RCSB], [https://www.ebi.ac.uk/pdbsum/6zcn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zcn 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;">
		+	== Publication Abstract from PubMed ==
		+	N6-Methyladenosine (m(6)A) is the most frequent modification in eukaryotic messenger RNA (mRNA) and its cellular processing and functions are regulated by the reader proteins YTHDCs and YTHDFs. However, the mechanism of m(6)A recognition by the reader proteins is still elusive. Here, we investigate this recognition process by combining atomistic simulations, site-directed mutagenesis, and biophysical experiments using YTHDC1 as a model. We find that the N6 methyl group of m(6)A contributes to the binding through its specific interactions with an aromatic cage (formed by Trp377 and Trp428) and also by favoring the association-prone conformation of m(6)A-containing RNA in solution. The m(6)A binding site dynamically equilibrates between multiple metastable conformations with four residues being involved in the regulation of m(6)A binding (Trp428, Met438, Ser378, and Thr379). Trp428 switches between two conformational states to build and dismantle the aromatic cage. Interestingly, mutating Met438 and Ser378 to alanine does not alter m(6)A binding to the protein but significantly redistributes the binding enthalpy and entropy terms, i.e., enthalpy-entropy compensation. Such compensation is reasoned by different entropy-enthalpy transduction associated with both conformational changes of the wild-type and mutant proteins and the redistribution of water molecules. In contrast, the point mutant Thr379Val significantly changes the thermal stability and binding capability of YTHDC1 to its natural ligand. Additionally, thermodynamic analysis and free energy calculations shed light on the role of a structural water molecule that synergistically binds to YTHDC1 with m(6)A and acts as the hub of a hydrogen-bond network. Taken together, the experimental data and simulation results may accelerate the discovery of chemical probes, m(6)A-editing tools, and drug candidates against reader proteins.
		+
		+	Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m(6)A) Recognition by the Reader Domain of YTHDC1.,Li Y, Bedi RK, Wiedmer L, Sun X, Huang D, Caflisch A J Chem Theory Comput. 2021 Feb 9;17(2):1240-1249. doi: 10.1021/acs.jctc.0c01136. , Epub 2021 Jan 20. PMID:33472367<ref>PMID:33472367</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zcn" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:02, 20 January 2021

OCA — Wed, 20 Jan 2021 06:02:53 GMT

←Older revision		Revision as of 06:02, 20 January 2021
Line 1:		Line 1:

	==Crystal structure of YTHDC1 with m6A==		==Crystal structure of YTHDC1 with m6A==
-	<StructureSection load='6zcn' size='340' side='right'caption='[[6zcn]]' scene=''>	+	<StructureSection load='6zcn' size='340' side='right'caption='[[6zcn]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZCN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZCN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zcn]] is a 2 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=6ZCN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZCN FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zcn OCA], [http://pdbe.org/6zcn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zcn RCSB], [http://www.ebi.ac.uk/pdbsum/6zcn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zcn ProSAT]</span></td></tr>	+	</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'>[http://proteopedia.org/fgij/fg.htm?mol=6zcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zcn OCA], [http://pdbe.org/6zcn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zcn RCSB], [http://www.ebi.ac.uk/pdbsum/6zcn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zcn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YTDC1_HUMAN YTDC1_HUMAN]] RNA-binding protein that regulates alternative splice site selection.<ref>PMID:20167602</ref>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bedi RK]]	+	[[Category: Bedi, R K]]
-	[[Category: Caflisch A]]	+	[[Category: Caflisch, A]]
-	[[Category: Huang D]]	+	[[Category: Huang, D]]
-	[[Category: Wiedmer L]]	+	[[Category: Wiedmer, L]]
		+	[[Category: Complex]]
		+	[[Category: Inhibitor]]
		+	[[Category: M6a]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Ythdc1]]

OCA at 11:12, 29 July 2020

OCA — Wed, 29 Jul 2020 11:12:36 GMT

←Older revision		Revision as of 11:12, 29 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6zcn ~~is ON HOLD~~	+	==Crystal structure of YTHDC1 with m6A==
-		+	<StructureSection load='6zcn' size='340' side='right'caption='[[6zcn]]' scene=''>
-	~~Authors~~: ~~Bedi~~, R.K., ~~Huang~~, D., ~~Wiedmer, L~~., ~~Caflisch, A~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZCN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZCN FirstGlance]. <br>
-	~~Description: Crystal structure of YTHDC1 with m6A~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zcn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zcn OCA], [http://pdbe.org/6zcn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zcn RCSB], [http://www.ebi.ac.uk/pdbsum/6zcn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zcn ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Caflisch, A~~]]	+	__TOC__
-	[[Category: ~~Bedi, R.K~~]]	+	</StructureSection>
-	[[Category: ~~Wiedmer, L~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Huang, D~~]]	+	[[Category: Bedi RK]]
		+	[[Category: Caflisch A]]
		+	[[Category: Huang D]]
		+	[[Category: Wiedmer L]]

OCA: Protected "6zcn" [edit=sysop:move=sysop]

OCA — Wed, 17 Jun 2020 08:57:25 GMT

Protected "6zcn" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:57, 17 June 2020

OCA: New page: '''Unreleased structure''' The entry 6zcn is ON HOLD Authors: Bedi, R.K., Huang, D., Wiedmer, L., Caflisch, A. Description: Crystal structure of YTHDC1 with m6A [[Category: Unreleased ...

OCA — Wed, 17 Jun 2020 08:57:24 GMT

New page: '''Unreleased structure''' The entry 6zcn is ON HOLD Authors: Bedi, R.K., Huang, D., Wiedmer, L., Caflisch, A. Description: Crystal structure of YTHDC1 with m6A [[Category: Unreleased ...

New page

'''Unreleased structure'''

The entry 6zcn is ON HOLD

Authors: Bedi, R.K., Huang, D., Wiedmer, L., Caflisch, A.

Description: Crystal structure of YTHDC1 with m6A
[[Category: Unreleased Structures]]
[[Category: Caflisch, A]]
[[Category: Bedi, R.K]]
[[Category: Wiedmer, L]]
[[Category: Huang, D]]