6lz8 - Revision history

OCA at 15:05, 29 November 2023

OCA — Wed, 29 Nov 2023 15:05:56 GMT

←Older revision		Revision as of 15:05, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6lz8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Middle_East_respiratory_syndrome-related_coronavirus Middle East respiratory syndrome-related coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LZ8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6lz8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Middle_East_respiratory_syndrome-related_coronavirus Middle East respiratory syndrome-related coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LZ8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EY9:5-(2-methoxyethoxy)-1H-indole'>EY9</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]] 2.59Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EY9:5-(2-methoxyethoxy)-1H-indole'>EY9</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=6lz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lz8 OCA], [https://pdbe.org/6lz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lz8 RCSB], [https://www.ebi.ac.uk/pdbsum/6lz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lz8 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=6lz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lz8 OCA], [https://pdbe.org/6lz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lz8 RCSB], [https://www.ebi.ac.uk/pdbsum/6lz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lz8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NCAP_MERS1 NCAP_MERS1]] 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.[HAMAP-Rule:MF_04096]	+	[https://www.uniprot.org/uniprot/NCAP_MERS1 NCAP_MERS1] 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.[HAMAP-Rule:MF_04096]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 18:52, 7 September 2022

OCA — Wed, 07 Sep 2022 18:52:36 GMT

←Older revision		Revision as of 18:52, 7 September 2022
Line 9:		Line 9:
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/NCAP_MERS1 NCAP_MERS1]] 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.[HAMAP-Rule:MF_04096]		[[https://www.uniprot.org/uniprot/NCAP_MERS1 NCAP_MERS1]] 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.[HAMAP-Rule:MF_04096]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Epidemics caused by coronaviruses (CoVs), namely the severe acute respiratory syndrome (SARS) (2003), Middle East respiratory syndrome (MERS) (2012), and coronavirus disease 2019 (COVID-19) (2019), have triggered a global public health emergency. Drug development against CoVs is inherently arduous. The nucleocapsid (N) protein forms an oligomer and facilitates binding with the viral RNA genome, which is critical in the life cycle of the virus. In the current study, we found a potential allosteric site (Site 1) using PARS, an online allosteric site predictor, in the CoV N-N-terminal RNA-binding domain (NTD) to modulate the N protein conformation. We identified 5-hydroxyindole as the lead via molecular docking to target Site 1. We designed and synthesized four 5-hydroxyindole derivatives, named P4-1 to P4-4, based on the pose of 5-hydroxyindole in the docking model complex. Small-angle X-ray scattering (SAXS) data indicate that two 5-hydroxyindole compounds with higher hydrophobic R-groups mediate the binding between N-NTD and N-C-terminal dimerization domain (CTD) and elicit high-order oligomerization of the whole N protein. Furthermore, the crystal structures suggested that these two compounds act on this novel cavity and create a flat surface with higher hydrophobicity, which may mediate the interaction between N-NTD and N-CTD. Taken together, we discovered an allosteric binding pocket targeting small molecules that induces abnormal aggregation of the CoV N protein. These novel concepts will facilitate protein-protein interaction (PPI)-based drug design against various CoVs.
		+
		+	Targeting the N-Terminus Domain of the Coronavirus Nucleocapsid Protein Induces Abnormal Oligomerization via Allosteric Modulation.,Hsu JN, Chen JS, Lin SM, Hong JY, Chen YJ, Jeng US, Luo SY, Hou MH Front Mol Biosci. 2022 Apr 19;9:871499. doi: 10.3389/fmolb.2022.871499., eCollection 2022. PMID:35517857<ref>PMID:35517857</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6lz8" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]		*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:46, 7 September 2022

OCA — Wed, 07 Sep 2022 16:46:03 GMT

←Older revision		Revision as of 16:46, 7 September 2022
Line 1:		Line 1:

	==Crystal structure of MERS-CoV N-NTD complexed with ligand P4-4==		==Crystal structure of MERS-CoV N-NTD complexed with ligand P4-4==
-	<StructureSection load='6lz8' size='340' side='right'caption='[[6lz8]]' scene=''>	+	<StructureSection load='6lz8' size='340' side='right'caption='[[6lz8]], [[Resolution\|resolution]] 2.59Å' 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=6LZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LZ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lz8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Middle_East_respiratory_syndrome-related_coronavirus Middle East respiratory syndrome-related coronavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LZ8 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=6lz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lz8 OCA], [https://pdbe.org/6lz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lz8 RCSB], [https://www.ebi.ac.uk/pdbsum/6lz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lz8 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=EY9:5-(2-methoxyethoxy)-1H-indole'>EY9</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=6lz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lz8 OCA], [https://pdbe.org/6lz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lz8 RCSB], [https://www.ebi.ac.uk/pdbsum/6lz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lz8 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/NCAP_MERS1 NCAP_MERS1]] 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.[HAMAP-Rule:MF_04096]
		+
		+	==See Also==
		+	*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Middle East respiratory syndrome-related coronavirus]]
	[[Category: Hou MH]]		[[Category: Hou MH]]
	[[Category: Hsu JN]]		[[Category: Hsu JN]]
	[[Category: Lin SM]]		[[Category: Lin SM]]

OCA at 06:38, 24 February 2021

OCA — Wed, 24 Feb 2021 06:38:03 GMT

←Older revision		Revision as of 06:38, 24 February 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6lz8 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of MERS-CoV N-NTD complexed with ligand P4-4==
-		+	<StructureSection load='6lz8' size='340' side='right'caption='[[6lz8]]' scene=''>
-	~~Authors~~: ~~Hou~~, M.H., ~~Lin~~, S.M., ~~Hsu~~, J.N.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LZ8 FirstGlance]. <br>
-	~~Description: Crystal structure of MERS-CoV N-NTD complexed with ligand P4-4~~	+	</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=6lz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lz8 OCA], [https://pdbe.org/6lz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lz8 RCSB], [https://www.ebi.ac.uk/pdbsum/6lz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lz8 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Hou~~, M.H~~]]	+	__TOC__
-	[[Category: Hsu~~, J.N~~]]	+	</StructureSection>
-	[[Category: Lin~~, S.M~~]]	+	[[Category: Large Structures]]
		+	[[Category: Hou MH]]
		+	[[Category: Hsu JN]]
		+	[[Category: Lin SM]]

OCA: Protected "6lz8" [edit=sysop:move=sysop]

OCA — Wed, 26 Feb 2020 08:01:42 GMT

Protected "6lz8" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:01, 26 February 2020

OCA: New page: '''Unreleased structure''' The entry 6lz8 is ON HOLD until Paper Publication Authors: Hou, M.H., Lin, S.M., Hsu, J.N. Description: Crystal structure of MERS-CoV N-NTD complexed with li...

OCA — Wed, 26 Feb 2020 08:01:40 GMT

New page: '''Unreleased structure''' The entry 6lz8 is ON HOLD until Paper Publication Authors: Hou, M.H., Lin, S.M., Hsu, J.N. Description: Crystal structure of MERS-CoV N-NTD complexed with li...

New page

'''Unreleased structure'''

The entry 6lz8 is ON HOLD until Paper Publication

Authors: Hou, M.H., Lin, S.M., Hsu, J.N.

Description: Crystal structure of MERS-CoV N-NTD complexed with ligand P4-4
[[Category: Unreleased Structures]]
[[Category: Hou, M.H]]
[[Category: Hsu, J.N]]
[[Category: Lin, S.M]]