6iic - Revision history

OCA at 10:33, 27 March 2024

OCA — Wed, 27 Mar 2024 10:33:30 GMT

←Older revision		Revision as of 10:33, 27 March 2024
Line 3:		Line 3:
	<SX load='6iic' size='340' side='right' viewer='molstar' caption='[[6iic]], [[Resolution\|resolution]] 3.30Å' scene=''>		<SX load='6iic' size='340' side='right' viewer='molstar' caption='[[6iic]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6iic]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Mud_crab_virus Mud crab virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IIC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6IIC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6iic]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mud_crab_virus Mud crab virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IIC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IIC 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=6iic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iic OCA], [~~http~~://pdbe.org/6iic PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6iic RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6iic PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6iic ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.3Å</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=6iic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iic OCA], [https://pdbe.org/6iic PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iic RCSB], [https://www.ebi.ac.uk/pdbsum/6iic PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iic ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/E5G7H9_9VIRU E5G7H9_9VIRU]
-	Viruses associated with sleeping disease (SD) in crabs cause great economic losses to aquaculture, and no effective measures are available for their prevention. In this study, to help develop novel antiviral strategies, single-particle cryo-electron microscopy was applied to investigate viruses associated with SD. The results not only revealed the structure of mud crab dicistrovirus (MCDV) but also identified a novel mud crab tombus-like virus (MCTV) not previously detected using molecular biology methods. The structure of MCDV at a 3.5-A resolution reveals three major capsid proteins (VP1 to VP3) organized into a pseudo-T=3 icosahedral capsid, and affirms the existence of VP4. Unusually, MCDV VP3 contains a long C-terminal region and forms a novel protrusion that has not been observed in other dicistrovirus. Our results also reveal that MCDV can release its genome via conformation changes of the protrusions when viral mixtures are heated. The structure of MCTV at a 3.3-A resolution reveals a T= 3 icosahedral capsid with common features of both tombusviruses and nodaviruses. Furthermore, MCTV has a novel hydrophobic tunnel beneath the 5-fold vertex and 30 dimeric protrusions composed of the P-domains of the capsid protein at the 2-fold axes that are exposed on the virion surface. The structural features of MCTV are consistent with a novel type of virus.IMPORTANCE Pathogen identification is vital for unknown infectious outbreaks, especially for dual or multiple infections. Sleeping disease (SD) in crabs causes great economic losses to aquaculture worldwide. Here we report the discovery and identification of a novel virus in mud crabs with multiple infections that was not previously detected by molecular, immune, or traditional electron microscopy (EM) methods. High-resolution structures of pathogenic viruses are essential for a molecular understanding and developing new disease prevention methods. The three-dimensional (3D) structure of the mud crab tombus-like virus (MCTV) and mud crab dicistrovirus (MCDV) determined in this study could assist the development of antiviral inhibitors. The identification of a novel virus in multiple infections previously missed using other methods demonstrates the usefulness of this strategy for investigating multiple infectious outbreaks, even in humans and other animals.	+
-		+
-	Cryo-electron Microscopy Structures of Novel Viruses from Mud Crab Scylla paramamosain with Multiple Infections.,Gao Y, Liu S, Huang J, Wang Q, Li K, He J, He J, Weng S, Zhang Q J Virol. 2019 Mar 21;93(7). pii: ~~JVI.02255-18. doi: 10.1128~~/~~JVI.02255-18. Print, 2019 Apr 1. PMID:30651355<ref>PMID:30651355<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6iic" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</SX>		</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Mud crab virus]]		[[Category: Mud crab virus]]
-	[[Category: Gao, Y]]	+	[[Category: Gao Y]]
-	[[Category: Zhang, Q]]	+	[[Category: Zhang Q]]
-	~~[[Category: Dicistrovirus]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 01:46, 11 April 2020

OCA — Sat, 11 Apr 2020 01:46:24 GMT

←Older revision		Revision as of 01:46, 11 April 2020
Line 3:		Line 3:
	<SX load='6iic' size='340' side='right' viewer='molstar' caption='[[6iic]], [[Resolution\|resolution]] 3.30Å' scene=''>		<SX load='6iic' size='340' side='right' viewer='molstar' caption='[[6iic]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6iic]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mud_crab_virus Mud crab virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IIC OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IIC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6iic]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mud_crab_virus Mud crab virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IIC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6IIC FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6iic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iic OCA], [http://pdbe.org/6iic PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iic RCSB], [http://www.ebi.ac.uk/pdbsum/6iic PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iic ProSAT]</span></td></tr>	+	</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=6iic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iic OCA], [http://pdbe.org/6iic PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iic RCSB], [http://www.ebi.ac.uk/pdbsum/6iic PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iic ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:08, 6 March 2020

OCA — Fri, 06 Mar 2020 22:08:37 GMT

←Older revision		Revision as of 22:08, 6 March 2020
Line 1:		Line 1:

	==CryoEM structure of Mud Crab Dicistrovirus==		==CryoEM structure of Mud Crab Dicistrovirus==
-	<~~StructureSection~~ load='6iic' size='340' side='right'caption='[[6iic]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<SX load='6iic' size='340' side='right' viewer='molstar' caption='[[6iic]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6iic]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mud_crab_virus Mud crab virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IIC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IIC FirstGlance]. <br>		<table><tr><td colspan='2'>[[6iic]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mud_crab_virus Mud crab virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IIC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IIC FirstGlance]. <br>
Line 18:		Line 18:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Mud crab virus]]		[[Category: Mud crab virus]]

OCA at 08:18, 3 April 2019

OCA — Wed, 03 Apr 2019 08:18:56 GMT

←Older revision		Revision as of 08:18, 3 April 2019
Line 1:		Line 1:

	==CryoEM structure of Mud Crab Dicistrovirus==		==CryoEM structure of Mud Crab Dicistrovirus==
-	<StructureSection load='6iic' size='340' side='right' caption='[[6iic]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<StructureSection load='6iic' size='340' side='right'caption='[[6iic]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6iic]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mud_crab_virus Mud crab virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IIC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IIC FirstGlance]. <br>		<table><tr><td colspan='2'>[[6iic]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mud_crab_virus Mud crab virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IIC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IIC FirstGlance]. <br>
	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6iic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iic OCA], [http://pdbe.org/6iic PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iic RCSB], [http://www.ebi.ac.uk/pdbsum/6iic PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iic ProSAT]</span></td></tr>		</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6iic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iic OCA], [http://pdbe.org/6iic PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iic RCSB], [http://www.ebi.ac.uk/pdbsum/6iic PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iic ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Viruses associated with sleeping disease (SD) in crabs cause great economic losses to aquaculture, and no effective measures are available for their prevention. In this study, to help develop novel antiviral strategies, single-particle cryo-electron microscopy was applied to investigate viruses associated with SD. The results not only revealed the structure of mud crab dicistrovirus (MCDV) but also identified a novel mud crab tombus-like virus (MCTV) not previously detected using molecular biology methods. The structure of MCDV at a 3.5-A resolution reveals three major capsid proteins (VP1 to VP3) organized into a pseudo-T=3 icosahedral capsid, and affirms the existence of VP4. Unusually, MCDV VP3 contains a long C-terminal region and forms a novel protrusion that has not been observed in other dicistrovirus. Our results also reveal that MCDV can release its genome via conformation changes of the protrusions when viral mixtures are heated. The structure of MCTV at a 3.3-A resolution reveals a T= 3 icosahedral capsid with common features of both tombusviruses and nodaviruses. Furthermore, MCTV has a novel hydrophobic tunnel beneath the 5-fold vertex and 30 dimeric protrusions composed of the P-domains of the capsid protein at the 2-fold axes that are exposed on the virion surface. The structural features of MCTV are consistent with a novel type of virus.IMPORTANCE Pathogen identification is vital for unknown infectious outbreaks, especially for dual or multiple infections. Sleeping disease (SD) in crabs causes great economic losses to aquaculture worldwide. Here we report the discovery and identification of a novel virus in mud crabs with multiple infections that was not previously detected by molecular, immune, or traditional electron microscopy (EM) methods. High-resolution structures of pathogenic viruses are essential for a molecular understanding and developing new disease prevention methods. The three-dimensional (3D) structure of the mud crab tombus-like virus (MCTV) and mud crab dicistrovirus (MCDV) determined in this study could assist the development of antiviral inhibitors. The identification of a novel virus in multiple infections previously missed using other methods demonstrates the usefulness of this strategy for investigating multiple infectious outbreaks, even in humans and other animals.
		+
		+	Cryo-electron Microscopy Structures of Novel Viruses from Mud Crab Scylla paramamosain with Multiple Infections.,Gao Y, Liu S, Huang J, Wang Q, Li K, He J, He J, Weng S, Zhang Q J Virol. 2019 Mar 21;93(7). pii: JVI.02255-18. doi: 10.1128/JVI.02255-18. Print, 2019 Apr 1. PMID:30651355<ref>PMID:30651355</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6iic" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mud crab virus]]		[[Category: Mud crab virus]]
	[[Category: Gao, Y]]		[[Category: Gao, Y]]

OCA at 12:11, 16 January 2019

OCA — Wed, 16 Jan 2019 12:11:45 GMT

←Older revision		Revision as of 12:11, 16 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6iic ~~is ON HOLD~~	+	==CryoEM structure of Mud Crab Dicistrovirus==
-		+	<StructureSection load='6iic' size='340' side='right' caption='[[6iic]], [[Resolution\|resolution]] 3.30Å' scene=''>
-	~~Authors~~: ~~Zhang~~, Q., ~~Gao~~, Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6iic]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mud_crab_virus Mud crab virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IIC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IIC FirstGlance]. <br>
-	~~Description: CryoEM structure of Mud Crab Dicistrovirus~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6iic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iic OCA], [http://pdbe.org/6iic PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iic RCSB], [http://www.ebi.ac.uk/pdbsum/6iic PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iic ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Mud crab virus]]
	[[Category: Gao, Y]]		[[Category: Gao, Y]]
	[[Category: Zhang, Q]]		[[Category: Zhang, Q]]
		+	[[Category: Dicistrovirus]]
		+	[[Category: Virus]]

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

OCA — Wed, 10 Oct 2018 06:25:26 GMT

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

←Older revision

Revision as of 06:25, 10 October 2018

OCA: New page: '''Unreleased structure''' The entry 6iic is ON HOLD Authors: Zhang, Q., Gao, Y. Description: CryoEM structure of Mud Crab Dicistrovirus Category: Unreleased Structures [[Category:...

OCA — Wed, 10 Oct 2018 06:25:25 GMT

New page: '''Unreleased structure''' The entry 6iic is ON HOLD Authors: Zhang, Q., Gao, Y. Description: CryoEM structure of Mud Crab Dicistrovirus Category: Unreleased Structures [[Category:...

New page

'''Unreleased structure'''

The entry 6iic is ON HOLD

Authors: Zhang, Q., Gao, Y.

Description: CryoEM structure of Mud Crab Dicistrovirus
[[Category: Unreleased Structures]]
[[Category: Gao, Y]]
[[Category: Zhang, Q]]