6m12 - Revision history

OCA at 15:09, 29 November 2023

OCA — Wed, 29 Nov 2023 15:09:41 GMT

←Older revision		Revision as of 15:09, 29 November 2023
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	<StructureSection load='6m12' size='340' side='right'caption='[[6m12]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6m12' size='340' side='right'caption='[[6m12]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m12]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pig Pig~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M12 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6M12 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m12]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M12 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=25L:[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-3-HYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-3-HYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]+PHOSPHONO+HYDROGEN+PHOSPHATE'>25L</scene>, <scene name='pdbligand=J60:5-[(E)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-N-[2-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE'>J60</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.4Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNASEL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=25L:[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-3-HYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-3-HYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]+PHOSPHONO+HYDROGEN+PHOSPHATE'>25L</scene>, <scene name='pdbligand=J60:5-[(E)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-N-[2-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE'>J60</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=6m12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m12 OCA], [~~http~~://pdbe.org/6m12 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6m12 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6m12 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6m12 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=6m12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m12 OCA], [https://pdbe.org/6m12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m12 RCSB], [https://www.ebi.ac.uk/pdbsum/6m12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m12 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A5H025_PIG A5H025_PIG]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6m12" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6m12" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pig~~]]	+	[[Category: Sus scrofa]]
-	[[Category: Huang, H]]	+	[[Category: Huang H]]
-	[[Category: Tang, J]]	+	[[Category: Tang J]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Rnase l]]~~	+
-	~~[[Category: Su11652~~]]	+

OCA at 07:22, 30 September 2020

OCA — Wed, 30 Sep 2020 07:22:19 GMT

←Older revision		Revision as of 07:22, 30 September 2020
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	==Crystal Structure of Rnase L in complex with SU11652==		==Crystal Structure of Rnase L in complex with SU11652==
-	<StructureSection load='6m12' size='340' side='right'caption='[[6m12]]' scene=''>	+	<StructureSection load='6m12' size='340' side='right'caption='[[6m12]], [[Resolution\|resolution]] 2.40Å' 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=6M12 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M12 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m12]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M12 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M12 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=6m12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m12 OCA], [http://pdbe.org/6m12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m12 RCSB], [http://www.ebi.ac.uk/pdbsum/6m12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m12 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=25L:[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-[[(2R,3R,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-3-HYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-3-HYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]+PHOSPHONO+HYDROGEN+PHOSPHATE'>25L</scene>, <scene name='pdbligand=J60:5-[(E)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-N-[2-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE'>J60</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNASEL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</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=6m12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m12 OCA], [http://pdbe.org/6m12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m12 RCSB], [http://www.ebi.ac.uk/pdbsum/6m12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m12 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The pseudokinase (PK) RNase L is a functional ribonuclease and plays important roles in human innate immunity. The ribonuclease activity of RNase L can be regulated by the kinase inhibitor sunitinib. The combined use of oncolytic virus and sunitinib has been shown to exert synergistic effects in anticancer therapy. In this study, we aimed to uncover the mechanism of action through which sunitinib inhibits RNase L. We solved the crystal structures of RNase L in complex with sunitinib and its analogs toceranib and SU11652. Our results showed that sunitinib bound to the ATP-binding pocket of RNase L. Unexpectedly, the alphaA helix linking the ankyrin repeat-domain and the PK domain affected the binding mode of sunitinib and resulted in an unusual flipped orientation relative to other structures in PDB. Molecular dynamics simulations and dynamic light scattering results support that the binding of sunitinib in the PK domain destabilized the dimer conformation of RNase L and allosterically inhibited its ribonuclease activity. Our study suggested that dimer destabilization could be an effective strategy for the discovery of RNase L inhibitors and that targeting the ATP-binding pocket in the PK domain of RNase L was an efficient approach for modulating its ribonuclease activity.
		+
		+	Sunitinib inhibits RNase L by destabilizing its active dimer conformation.,Tang J, Wang Y, Zhou H, Ye Y, Talukdar M, Fu Z, Liu Z, Li J, Neculai D, Gao J, Huang H Biochem J. 2020 Sep 18;477(17):3387-3399. doi: 10.1042/BCJ20200260. PMID:32830849<ref>PMID:32830849</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6m12" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Huang H]]	+	[[Category: Pig]]
-	[[Category: Tang J]]	+	[[Category: Huang, H]]
		+	[[Category: Tang, J]]
		+	[[Category: Complex]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inhibitor]]
		+	[[Category: Rnase l]]
		+	[[Category: Su11652]]

OCA at 06:47, 2 September 2020

OCA — Wed, 02 Sep 2020 06:47:21 GMT

←Older revision		Revision as of 06:47, 2 September 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6m12 ~~is ON HOLD~~	+	==Crystal Structure of Rnase L in complex with SU11652==
-		+	<StructureSection load='6m12' size='340' side='right'caption='[[6m12]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M12 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M12 FirstGlance]. <br>
-	~~Description~~:	+	</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=6m12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m12 OCA], [http://pdbe.org/6m12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m12 RCSB], [http://www.ebi.ac.uk/pdbsum/6m12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m12 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Huang H]]
		+	[[Category: Tang J]]

OCA: Protected "6m12" [edit=sysop:move=sysop]

OCA — Wed, 04 Mar 2020 05:28:51 GMT

Protected "6m12" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:28, 4 March 2020

OCA: New page: '''Unreleased structure''' The entry 6m12 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 04 Mar 2020 05:28:50 GMT

New page: '''Unreleased structure''' The entry 6m12 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6m12 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]