7uxz - Revision history

OCA at 17:21, 18 October 2023

OCA — Wed, 18 Oct 2023 17:21:57 GMT

←Older revision		Revision as of 17:21, 18 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7uxz]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UXZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UXZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[7uxz]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UXZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UXZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GKP:(2R,3R)-2,3-bis{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}butanedioic+acid'>GKP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.733Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GKP:(2R,3R)-2,3-bis{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}butanedioic+acid'>GKP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=7uxz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uxz OCA], [https://pdbe.org/7uxz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uxz RCSB], [https://www.ebi.ac.uk/pdbsum/7uxz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uxz 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=7uxz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uxz OCA], [https://pdbe.org/7uxz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uxz RCSB], [https://www.ebi.ac.uk/pdbsum/7uxz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uxz ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 7uxz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7uxz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:26, 16 November 2022

OCA — Wed, 16 Nov 2022 20:26:30 GMT

←Older revision		Revision as of 20:26, 16 November 2022
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	==Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain complexed with Chicoric acid==		==Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain complexed with Chicoric acid==
-	<StructureSection load='7uxz' size='340' side='right'caption='[[7uxz]]' scene=''>	+	<StructureSection load='7uxz' size='340' side='right'caption='[[7uxz]], [[Resolution\|resolution]] 1.73Å' 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=7UXZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UXZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7uxz]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UXZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UXZ 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=7uxz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uxz OCA], [https://pdbe.org/7uxz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uxz RCSB], [https://www.ebi.ac.uk/pdbsum/7uxz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uxz 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GKP:(2R,3R)-2,3-bis{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}butanedioic+acid'>GKP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=7uxz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uxz OCA], [https://pdbe.org/7uxz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uxz RCSB], [https://www.ebi.ac.uk/pdbsum/7uxz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uxz ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/NCAP_SARS2 NCAP_SARS2] Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The nucleocapsid (N) protein plays critical roles in coronavirus genome transcription and packaging, representing a key target for the development of novel antivirals, and for which structural information on ligand binding is scarce. We used a novel fluorescence polarization assay to identify small molecules that disrupt the binding of the N protein to a target RNA derived from the SARS-CoV-2 genome packaging signal. Several phenolic compounds, including L-chicoric acid (CA), were identified as high-affinity N-protein ligands. The binding of CA to the N protein was confirmed by isothermal titration calorimetry, (1)H-STD and (15)N-HSQC NMR, and by the crystal structure of CA bound to the N protein C-terminal domain (CTD), further revealing a new modulatory site in the SARS-CoV-2 N protein. Moreover, CA reduced SARS-CoV-2 replication in cell cultures. These data thus open venues for the development of new antivirals targeting the N protein, an essential and yet underexplored coronavirus target.
		+
		+	Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor.,Mercaldi GF, Bezerra EHS, Batista FAH, Tonoli CCC, Soprano AS, Shimizu JF, Nagai A, da Silva JC, Filho HVR, do Nascimento Faria J, da Cunha MG, Zeri ACM, Nascimento AFZ, Proenca-Modena JL, Bajgelman MC, Rocco SA, Lopes-de-Oliveira PS, Cordeiro AT, Bruder M, Marques RE, Sforca ML, Franchini KG, Benedetti CE, Figueira ACM, Trivella DBB Sci Rep. 2022 Nov 2;12(1):18500. doi: 10.1038/s41598-022-22576-4. PMID:36323732<ref>PMID:36323732</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7uxz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
	[[Category: Benedetti CE]]		[[Category: Benedetti CE]]
	[[Category: Bezerra EHS]]		[[Category: Bezerra EHS]]

OCA at 09:46, 22 June 2022

OCA — Wed, 22 Jun 2022 09:46:31 GMT

←Older revision		Revision as of 09:46, 22 June 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7uxz ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain complexed with Chicoric acid==
-		+	<StructureSection load='7uxz' size='340' side='right'caption='[[7uxz]]' scene=''>
-	~~Authors~~: ~~Bezerra, E~~.H.S.~~, Tonoli, C~~.C.C., ~~Soprano, A~~.S., ~~Franchini~~, K.G., ~~Trivella, D~~.B.B., ~~Benedetti, C~~.E.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UXZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UXZ FirstGlance]. <br>
-	~~Description: Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain complexed with Chicoric acid~~	+	</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=7uxz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uxz OCA], [https://pdbe.org/7uxz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uxz RCSB], [https://www.ebi.ac.uk/pdbsum/7uxz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uxz ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Franchini, K.G~~]]	+	__TOC__
-	[[Category: ~~Benedetti, C.E~~]]	+	</StructureSection>
-	[[Category: ~~Tonoli, C.C.C~~]]	+	[[Category: Large Structures]]
-	[[Category: Soprano~~, A.S~~]]	+	[[Category: Benedetti CE]]
-	[[Category: ~~Trivella, D.B.B~~]]	+	[[Category: Bezerra EHS]]
-	[[Category: ~~Bezerra, E.H.S~~]]	+	[[Category: Franchini KG]]
		+	[[Category: Soprano AS]]
		+	[[Category: Tonoli CCC]]
		+	[[Category: Trivella DBB]]

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

OCA — Wed, 18 May 2022 09:02:43 GMT

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

←Older revision

Revision as of 09:02, 18 May 2022

OCA: New page: '''Unreleased structure''' The entry 7uxz is ON HOLD until Paper Publication Authors: Bezerra, E.H.S., Tonoli, C.C.C., Soprano, A.S., Franchini, K.G., Trivella, D.B.B., Benedetti, C.E. ...

OCA — Wed, 18 May 2022 09:02:42 GMT

New page: '''Unreleased structure''' The entry 7uxz is ON HOLD until Paper Publication Authors: Bezerra, E.H.S., Tonoli, C.C.C., Soprano, A.S., Franchini, K.G., Trivella, D.B.B., Benedetti, C.E. ...

New page

'''Unreleased structure'''

The entry 7uxz is ON HOLD until Paper Publication

Authors: Bezerra, E.H.S., Tonoli, C.C.C., Soprano, A.S., Franchini, K.G., Trivella, D.B.B., Benedetti, C.E.

Description: Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain complexed with Chicoric acid
[[Category: Unreleased Structures]]
[[Category: Franchini, K.G]]
[[Category: Benedetti, C.E]]
[[Category: Tonoli, C.C.C]]
[[Category: Soprano, A.S]]
[[Category: Trivella, D.B.B]]
[[Category: Bezerra, E.H.S]]