5yl1 - Revision history

OCA at 10:23, 27 March 2024

2024-03-27T10:23:54Z

←Older revision		Revision as of 10:23, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5yl1' size='340' side='right'caption='[[5yl1]], [[Resolution\|resolution]] 3.12Å' scene=''>		<StructureSection load='5yl1' size='340' side='right'caption='[[5yl1]], [[Resolution\|resolution]] 3.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yl1]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Litopenaeus_vannamei_nodavirus Litopenaeus~~ vannamei nodavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YL1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YL1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yl1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Penaeus_vannamei_nodavirus Penaeus vannamei nodavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YL1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YL1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 3.12Å</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=5yl1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yl1 OCA], [~~http~~://pdbe.org/5yl1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yl1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yl1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yl1 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=5yl1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yl1 OCA], [https://pdbe.org/5yl1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yl1 RCSB], [https://www.ebi.ac.uk/pdbsum/5yl1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yl1 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A5H7Q8_9VIRU A5H7Q8_9VIRU]
-	Shrimp nodaviruses, including Penaeus vannamei (PvNV) and Macrobrachium rosenbergii nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of T = 3 and T = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the N-ARM-PvNV shell-domain (S-domain) in T = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic N-terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls T = 3 and T = 1 assemblies. Increasing the N/~~C-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement.~~	+
-		+
-	The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.,Chen NC, Yoshimura M, Miyazaki N, Guan HH, Chuankhayan P, Lin CC, Chen SK, Lin PJ, Huang YC, Iwasaki K, Nakagawa A, Chan SI, Chen CJ Commun Biol. 2019 Feb 20;2:72. doi: 10.1038/~~s42003-019-0311-z~~. ~~eCollection 2019~~. ~~PMID:30820467<ref>PMID:30820467<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5yl1" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Litopenaeus~~ vannamei nodavirus]]	+	[[Category: Penaeus vannamei nodavirus]]
-	[[Category: Chen~~, C J~~]]	+	[[Category: Chen CJ]]
-	[[Category: Chen~~, N C~~]]	+	[[Category: Chen NC]]
-	[[Category: Chuankhayan, P]]	+	[[Category: Chuankhayan P]]
-	[[Category: Guan~~, H H~~]]	+	[[Category: Guan HH]]
-	[[Category: Lin~~, C C~~]]	+	[[Category: Lin CC]]
-	[[Category: Yoshimura, M]]	+	[[Category: Yoshimura M]]
-	~~[[Category: Viral capsid protein]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 12:33, 13 March 2019

2019-03-13T12:33:34Z

←Older revision		Revision as of 12:33, 13 March 2019
Line 1:		Line 1:

	==T=1 subviral particle of Penaeus vannamei nodavirus capsid protein deletion mutant (delta 1-37 & 251-368)==		==T=1 subviral particle of Penaeus vannamei nodavirus capsid protein deletion mutant (delta 1-37 & 251-368)==
-	<StructureSection load='5yl1' size='340' side='right' caption='[[5yl1]], [[Resolution\|resolution]] 3.12Å' scene=''>	+	<StructureSection load='5yl1' size='340' side='right'caption='[[5yl1]], [[Resolution\|resolution]] 3.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5yl1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Litopenaeus_vannamei_nodavirus Litopenaeus vannamei nodavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YL1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YL1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5yl1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Litopenaeus_vannamei_nodavirus Litopenaeus vannamei nodavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YL1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YL1 FirstGlance]. <br>
Line 7:		Line 7:
	<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=5yl1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yl1 OCA], [http://pdbe.org/5yl1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yl1 RCSB], [http://www.ebi.ac.uk/pdbsum/5yl1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yl1 ProSAT]</span></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=5yl1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yl1 OCA], [http://pdbe.org/5yl1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yl1 RCSB], [http://www.ebi.ac.uk/pdbsum/5yl1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yl1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Shrimp nodaviruses, including Penaeus vannamei (PvNV) and Macrobrachium rosenbergii nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of T = 3 and T = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the N-ARM-PvNV shell-domain (S-domain) in T = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic N-terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls T = 3 and T = 1 assemblies. Increasing the N/C-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement.
		+
		+	The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.,Chen NC, Yoshimura M, Miyazaki N, Guan HH, Chuankhayan P, Lin CC, Chen SK, Lin PJ, Huang YC, Iwasaki K, Nakagawa A, Chan SI, Chen CJ Commun Biol. 2019 Feb 20;2:72. doi: 10.1038/s42003-019-0311-z. eCollection 2019. PMID:30820467<ref>PMID:30820467</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yl1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Litopenaeus vannamei nodavirus]]		[[Category: Litopenaeus vannamei nodavirus]]
	[[Category: Chen, C J]]		[[Category: Chen, C J]]

OCA at 15:52, 27 February 2019

2019-02-27T15:52:05Z

←Older revision		Revision as of 15:52, 27 February 2019
Line 3:		Line 3:
	<StructureSection load='5yl1' size='340' side='right' caption='[[5yl1]], [[Resolution\|resolution]] 3.12Å' scene=''>		<StructureSection load='5yl1' size='340' side='right' caption='[[5yl1]], [[Resolution\|resolution]] 3.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yl1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YL1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YL1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yl1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Litopenaeus_vannamei_nodavirus Litopenaeus vannamei nodavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YL1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YL1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=5yl1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yl1 OCA], [http://pdbe.org/5yl1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yl1 RCSB], [http://www.ebi.ac.uk/pdbsum/5yl1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yl1 ProSAT]</span></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=5yl1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yl1 OCA], [http://pdbe.org/5yl1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yl1 RCSB], [http://www.ebi.ac.uk/pdbsum/5yl1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yl1 ProSAT]</span></td></tr>
Line 9:		Line 9:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Litopenaeus vannamei nodavirus]]
	[[Category: Chen, C J]]		[[Category: Chen, C J]]
	[[Category: Chen, N C]]		[[Category: Chen, N C]]

OCA at 06:38, 12 December 2018

2018-12-12T06:38:22Z

←Older revision		Revision as of 06:38, 12 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5yl1 is ON HOLD until Paper Publication~~	+	==T=1 subviral particle of Penaeus vannamei nodavirus capsid protein deletion mutant (delta 1-37 & 251-368)==
-		+	<StructureSection load='5yl1' size='340' side='right' caption='[[5yl1]], [[Resolution\|resolution]] 3.12Å' scene=''>
-	~~Authors: Chen, N.C., Yoshimura, M., Lin, C.C., Guan, H.H., Chuankhayan, P., Chen, C.J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yl1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YL1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YL1 FirstGlance]. <br>
-	~~Description:~~ T=1 subviral particle of Penaeus vannamei nodavirus capsid protein deletion mutant (delta 1-37 & 251-368)	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5yl1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yl1 OCA], [http://pdbe.org/5yl1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yl1 RCSB], [http://www.ebi.ac.uk/pdbsum/5yl1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yl1 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Guan~~, H.H]]	+	</table>
-	[[Category: Chen, C.J]]	+	__TOC__
-	[[Category: Lin, C.C]]	+	</StructureSection>
		+	[[Category: Chen, C J]]
		+	[[Category: Chen, N C]]
		+	[[Category: Chuankhayan, P]]
		+	[[Category: Guan, H H]]
		+	[[Category: Lin, C C]]
	[[Category: Yoshimura, M]]		[[Category: Yoshimura, M]]
-	[[Category: ~~Chuankhayan, P~~]]	+	[[Category: Viral capsid protein]]
-	[[Category: ~~Chen, N.C~~]]	+	[[Category: Viral protein]]

OCA at 04:56, 5 December 2018

2018-12-05T04:56:06Z

←Older revision		Revision as of 04:56, 5 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yl1 is ON HOLD	+	The entry 5yl1 is ON HOLD until Paper Publication

	Authors: Chen, N.C., Yoshimura, M., Lin, C.C., Guan, H.H., Chuankhayan, P., Chen, C.J.		Authors: Chen, N.C., Yoshimura, M., Lin, C.C., Guan, H.H., Chuankhayan, P., Chen, C.J.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Guan, H.H]]		[[Category: Guan, H.H]]
		+	[[Category: Chen, C.J]]
	[[Category: Lin, C.C]]		[[Category: Lin, C.C]]
	[[Category: Yoshimura, M]]		[[Category: Yoshimura, M]]
-	[[Category: Chen, C.J]]
	[[Category: Chuankhayan, P]]		[[Category: Chuankhayan, P]]
	[[Category: Chen, N.C]]		[[Category: Chen, N.C]]

OCA at 03:34, 8 March 2018

2018-03-08T03:34:39Z

←Older revision		Revision as of 03:34, 8 March 2018
Line 7:		Line 7:
	Description: T=1 subviral particle of Penaeus vannamei nodavirus capsid protein deletion mutant (delta 1-37 & 251-368)		Description: T=1 subviral particle of Penaeus vannamei nodavirus capsid protein deletion mutant (delta 1-37 & 251-368)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Yoshimura, M]]
-	[[Category: Chen, N.C]]
	[[Category: Guan, H.H]]		[[Category: Guan, H.H]]
	[[Category: Lin, C.C]]		[[Category: Lin, C.C]]
		+	[[Category: Yoshimura, M]]
	[[Category: Chen, C.J]]		[[Category: Chen, C.J]]
	[[Category: Chuankhayan, P]]		[[Category: Chuankhayan, P]]
		+	[[Category: Chen, N.C]]

OCA: Protected "5yl1" [edit=sysop:move=sysop]

2017-10-25T05:39:22Z

Protected "5yl1" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:39, 25 October 2017

OCA: New page: '''Unreleased structure''' The entry 5yl1 is ON HOLD Authors: Chen, N.C., Yoshimura, M., Lin, C.C., Guan, H.H., Chuankhayan, P., Chen, C.J. Description: T=1 subviral particle of Penaeu...

2017-10-25T05:39:21Z

New page: '''Unreleased structure''' The entry 5yl1 is ON HOLD Authors: Chen, N.C., Yoshimura, M., Lin, C.C., Guan, H.H., Chuankhayan, P., Chen, C.J. Description: T=1 subviral particle of Penaeu...

New page

'''Unreleased structure'''

The entry 5yl1 is ON HOLD

Authors: Chen, N.C., Yoshimura, M., Lin, C.C., Guan, H.H., Chuankhayan, P., Chen, C.J.

Description: T=1 subviral particle of Penaeus vannamei nodavirus capsid protein deletion mutant (delta 1-37 & 251-368)
[[Category: Unreleased Structures]]
[[Category: Yoshimura, M]]
[[Category: Chen, N.C]]
[[Category: Guan, H.H]]
[[Category: Lin, C.C]]
[[Category: Chen, C.J]]
[[Category: Chuankhayan, P]]