7z26 - Revision history

OCA at 08:01, 7 February 2024

OCA — Wed, 07 Feb 2024 08:01:30 GMT

←Older revision		Revision as of 08:01, 7 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7z26]] 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=7Z26 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z26 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7z26]] 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=7Z26 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z26 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=GOL:GLYCEROL'>GOL</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]] 1.9Å</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=GOL:GLYCEROL'>GOL</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=7z26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z26 OCA], [https://pdbe.org/7z26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z26 RCSB], [https://www.ebi.ac.uk/pdbsum/7z26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z26 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=7z26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z26 OCA], [https://pdbe.org/7z26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z26 RCSB], [https://www.ebi.ac.uk/pdbsum/7z26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z26 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/YTHD2_HUMAN YTHD2_HUMAN] Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs. M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability. Acts as a regulator of mRNA stability: binding to m6A-containing mRNAs results in the localization of to mRNA decay sites, such as processing bodies (P-bodies), leading to mRNA degradation.<ref>PMID:22575960</ref> <ref>PMID:24284625</ref>		[https://www.uniprot.org/uniprot/YTHD2_HUMAN YTHD2_HUMAN] Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs. M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability. Acts as a regulator of mRNA stability: binding to m6A-containing mRNAs results in the localization of to mRNA decay sites, such as processing bodies (P-bodies), leading to mRNA degradation.<ref>PMID:22575960</ref> <ref>PMID:24284625</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	We report 17 small-molecule ligands that compete with N6-methyladenosine (m(6)A) for binding to the m(6)A-reader domain of YTHDF2 (YT521-B homology domain family 2). We determined their binding mode at high resolution by X-ray crystallography and quantified their affinity by a fluorescence-based binding assay. 6-Cyclopropyluracil and a pyrazolopyrimidine derivative have favorable ligand efficiencies of 0.47 and 0.38 kcal mol(-1) per non-hydrogen atom, respectively. They represent useful starting points for hit optimization.
-
-	Fragment Ligands of the m(6)A-RNA Reader YTHDF2.,Nai F, Nachawati R, Zalesak F, Wang X, Li Y, Caflisch A ACS Med Chem Lett. 2022 Aug 17;13(9):1500-1509. doi:, 10.1021/acsmedchemlett.2c00303. eCollection 2022 Sep 8. PMID:36110386<ref>PMID:36110386</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7z26" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:22, 14 June 2023

OCA — Wed, 14 Jun 2023 11:22:20 GMT

←Older revision		Revision as of 11:22, 14 June 2023
Line 8:		Line 8:
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/YTHD2_HUMAN YTHD2_HUMAN]] Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs. M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability. Acts as a regulator of mRNA stability: binding to m6A-containing mRNAs results in the localization of to mRNA decay sites, such as processing bodies (P-bodies), leading to mRNA degradation.<ref>PMID:22575960</ref> <ref>PMID:24284625</ref>	+	[https://www.uniprot.org/uniprot/YTHD2_HUMAN YTHD2_HUMAN] Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs. M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability. Acts as a regulator of mRNA stability: binding to m6A-containing mRNAs results in the localization of to mRNA decay sites, such as processing bodies (P-bodies), leading to mRNA degradation.<ref>PMID:22575960</ref> <ref>PMID:24284625</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 06:30, 28 September 2022

OCA — Wed, 28 Sep 2022 06:30:19 GMT

←Older revision		Revision as of 06:30, 28 September 2022
Line 1:		Line 1:

-	====	+	==Crystal structure of YTHDF2 YTH domain in complex with m6A RNA==
-	<StructureSection load='7z26' size='340' side='right'caption='[[7z26]]' scene=''>	+	<StructureSection load='7z26' size='340' side='right'caption='[[7z26]], [[Resolution\|resolution]] 1.90Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7z26]] 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=7Z26 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z26 FirstGlance]. <br>
-	</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=7z26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z26 OCA], [https://pdbe.org/7z26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z26 RCSB], [https://www.ebi.ac.uk/pdbsum/7z26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z26 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=GOL:GLYCEROL'>GOL</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=7z26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z26 OCA], [https://pdbe.org/7z26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z26 RCSB], [https://www.ebi.ac.uk/pdbsum/7z26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z26 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/YTHD2_HUMAN YTHD2_HUMAN]] Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs. M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability. Acts as a regulator of mRNA stability: binding to m6A-containing mRNAs results in the localization of to mRNA decay sites, such as processing bodies (P-bodies), leading to mRNA degradation.<ref>PMID:22575960</ref> <ref>PMID:24284625</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report 17 small-molecule ligands that compete with N6-methyladenosine (m(6)A) for binding to the m(6)A-reader domain of YTHDF2 (YT521-B homology domain family 2). We determined their binding mode at high resolution by X-ray crystallography and quantified their affinity by a fluorescence-based binding assay. 6-Cyclopropyluracil and a pyrazolopyrimidine derivative have favorable ligand efficiencies of 0.47 and 0.38 kcal mol(-1) per non-hydrogen atom, respectively. They represent useful starting points for hit optimization.
		+
		+	Fragment Ligands of the m(6)A-RNA Reader YTHDF2.,Nai F, Nachawati R, Zalesak F, Wang X, Li Y, Caflisch A ACS Med Chem Lett. 2022 Aug 17;13(9):1500-1509. doi:, 10.1021/acsmedchemlett.2c00303. eCollection 2022 Sep 8. PMID:36110386<ref>PMID:36110386</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7z26" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Caflisch A]]
		+	[[Category: Li Y]]
		+	[[Category: Nachawati R]]
		+	[[Category: Nai F]]

OCA at 06:19, 16 March 2022

OCA — Wed, 16 Mar 2022 06:19:06 GMT

←Older revision		Revision as of 06:19, 16 March 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7z26 ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7z26' size='340' side='right'caption='[[7z26]]' scene=''>
-	~~Authors~~: ~~Nai, F~~.~~, Nachawati, R~~.~~, Li, Y~~.~~, Caflisch, A~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description: Crystal~~ structure ~~of YTHDF2 YTH domain in complex with m6A RNA~~	+	</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=7z26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z26 OCA], [https://pdbe.org/7z26 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z26 RCSB], [https://www.ebi.ac.uk/pdbsum/7z26 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z26 ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures]~~]	+	</table>
-	[[~~Category~~: ~~Nai~~, F]]	+	__TOC__
-	[~~[Category~~: ~~Li, Y~~]]	+	</StructureSection>
-	[[Category: ~~Nachawati, R~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Caflisch, A~~]]	+	[[Category: Z-disk]]

OCA: Protected "7z26" [edit=sysop:move=sysop]

OCA — Wed, 09 Mar 2022 05:10:24 GMT

Protected "7z26" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:10, 9 March 2022

OCA: New page: '''Unreleased structure''' The entry 7z26 is ON HOLD Authors: Nai, F., Nachawati, R., Li, Y., Caflisch, A. Description: Crystal structure of YTHDF2 YTH domain in complex with m6A RNA [...

OCA — Wed, 09 Mar 2022 05:10:24 GMT

New page: '''Unreleased structure''' The entry 7z26 is ON HOLD Authors: Nai, F., Nachawati, R., Li, Y., Caflisch, A. Description: Crystal structure of YTHDF2 YTH domain in complex with m6A RNA [...

New page

'''Unreleased structure'''

The entry 7z26 is ON HOLD

Authors: Nai, F., Nachawati, R., Li, Y., Caflisch, A.

Description: Crystal structure of YTHDF2 YTH domain in complex with m6A RNA
[[Category: Unreleased Structures]]
[[Category: Nai, F]]
[[Category: Li, Y]]
[[Category: Nachawati, R]]
[[Category: Caflisch, A]]