6bjy - Revision history

OCA at 14:43, 4 October 2023

OCA — Wed, 04 Oct 2023 14:43:52 GMT

←Older revision		Revision as of 14:43, 4 October 2023
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	<StructureSection load='6bjy' size='340' side='right'caption='[[6bjy]], [[Resolution\|resolution]] 3.46Å' scene=''>		<StructureSection load='6bjy' size='340' side='right'caption='[[6bjy]], [[Resolution\|resolution]] 3.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bjy]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/ ] and [~~http~~://en.wikipedia.org/wiki/~~Vsiv Vsiv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6BJY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bjy]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Vesicular_stomatitis_Indiana_virus Vesicular stomatitis Indiana virus] and [https://en.wikipedia.org/wiki/Vesicular_stomatitis_Indiana_virus_strain_San_Juan Vesicular stomatitis Indiana virus strain San Juan]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BJY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DV4:4-{[4-(acetylamino)-1-methyl-1H-pyrrole-2-carbonyl]amino}-1-methyl-N-{4-[(1-methyl-1H-pyrrol-3-yl)amino]-4-oxobutyl}-1H-imidazole-2-carboxamide'>DV4</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</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]] 3.46Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gic\|2gic]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DV4:4-{[4-(acetylamino)-1-methyl-1H-pyrrole-2-carbonyl]amino}-1-methyl-N-{4-[(1-methyl-1H-pyrrol-3-yl)amino]-4-oxobutyl}-1H-imidazole-2-carboxamide'>DV4</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</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=6bjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bjy OCA], [~~http~~://pdbe.org/6bjy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bjy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bjy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bjy 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=6bjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bjy OCA], [https://pdbe.org/6bjy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bjy RCSB], [https://www.ebi.ac.uk/pdbsum/6bjy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bjy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NCAP_VSIVA NCAP_VSIVA]] Encapsidates the genome in a ratio of one N per nine ribonucleotides, protecting it from nucleases. The encapsidated genomic RNA is termed the NC and serves as template for transcription and replication. Replication is dependent on intracellular concentration of newly synthesized N, termed N(0), which corresponds to the protein not associated with RNA. In contrast, when associated with RNA, it is termed N. During replication, encapsidation by N(0) is coupled to RNA synthesis and all replicative products are resistant to nucleases (By similarity).	+	[https://www.uniprot.org/uniprot/NCAP_VSIVA NCAP_VSIVA] Encapsidates the genome in a ratio of one N per nine ribonucleotides, protecting it from nucleases. The encapsidated genomic RNA is termed the NC and serves as template for transcription and replication. Replication is dependent on intracellular concentration of newly synthesized N, termed N(0), which corresponds to the protein not associated with RNA. In contrast, when associated with RNA, it is termed N. During replication, encapsidation by N(0) is coupled to RNA synthesis and all replicative products are resistant to nucleases (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Vsiv~~]]	+	[[Category: Vesicular stomatitis Indiana virus]]
-	[[Category: ~~Gumpper, R H~~]]	+	[[Category: Vesicular stomatitis Indiana virus strain San Juan]]
-	[[Category: ~~Luo, M~~]]	+	[[Category: Gumpper RH]]
-	[[Category: ~~Nucleocapisd]]~~	+	[[Category: Luo M]]
-	~~[[Category: Nucleocapsid-like particle]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Rna binding protein-rna complex]]~~	+
-	~~[[Category: Vsv~~]]	+

OCA at 08:50, 11 November 2020

OCA — Wed, 11 Nov 2020 08:50:24 GMT

←Older revision		Revision as of 08:50, 11 November 2020
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	==VSV Nucleocapsid with Polyamide Bound==		==VSV Nucleocapsid with Polyamide Bound==
-	<StructureSection load='6bjy' size='340' side='right' caption='[[6bjy]], [[Resolution\|resolution]] 3.46Å' scene=''>	+	<StructureSection load='6bjy' size='340' side='right'caption='[[6bjy]], [[Resolution\|resolution]] 3.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bjy]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Vsiv Vsiv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BJY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bjy]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Vsiv Vsiv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6BJY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DV4:4-{[4-(acetylamino)-1-methyl-1H-pyrrole-2-carbonyl]amino}-1-methyl-N-{4-[(1-methyl-1H-pyrrol-3-yl)amino]-4-oxobutyl}-1H-imidazole-2-carboxamide'>DV4</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DV4:4-{[4-(acetylamino)-1-methyl-1H-pyrrole-2-carbonyl]amino}-1-methyl-N-{4-[(1-methyl-1H-pyrrol-3-yl)amino]-4-oxobutyl}-1H-imidazole-2-carboxamide'>DV4</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gic\|2gic]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gic\|2gic]]</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=6bjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bjy OCA], [http://pdbe.org/6bjy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bjy RCSB], [http://www.ebi.ac.uk/pdbsum/6bjy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bjy ProSAT]</span></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=6bjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bjy OCA], [http://pdbe.org/6bjy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bjy RCSB], [http://www.ebi.ac.uk/pdbsum/6bjy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bjy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6bjy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6bjy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Vsiv]]		[[Category: Vsiv]]
	[[Category: Gumpper, R H]]		[[Category: Gumpper, R H]]

OCA at 14:17, 11 April 2018

OCA — Wed, 11 Apr 2018 14:17:21 GMT

←Older revision		Revision as of 14:17, 11 April 2018
Line 3:		Line 3:
	<StructureSection load='6bjy' size='340' side='right' caption='[[6bjy]], [[Resolution\|resolution]] 3.46Å' scene=''>		<StructureSection load='6bjy' size='340' side='right' caption='[[6bjy]], [[Resolution\|resolution]] 3.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bjy]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BJY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bjy]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Vsiv Vsiv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BJY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DV4:4-{[4-(acetylamino)-1-methyl-1H-pyrrole-2-carbonyl]amino}-1-methyl-N-{4-[(1-methyl-1H-pyrrol-3-yl)amino]-4-oxobutyl}-1H-imidazole-2-carboxamide'>DV4</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DV4:4-{[4-(acetylamino)-1-methyl-1H-pyrrole-2-carbonyl]amino}-1-methyl-N-{4-[(1-methyl-1H-pyrrol-3-yl)amino]-4-oxobutyl}-1H-imidazole-2-carboxamide'>DV4</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gic\|2gic]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gic\|2gic]]</td></tr>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Vsiv]]
	[[Category: Gumpper, R H]]		[[Category: Gumpper, R H]]
	[[Category: Luo, M]]		[[Category: Luo, M]]

OCA at 06:32, 28 February 2018

OCA — Wed, 28 Feb 2018 06:32:07 GMT

←Older revision		Revision as of 06:32, 28 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6bjy is ~~ON HOLD until Paper~~ Publication	+	==VSV Nucleocapsid with Polyamide Bound==
		+	<StructureSection load='6bjy' size='340' side='right' caption='[[6bjy]], [[Resolution\|resolution]] 3.46Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6bjy]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BJY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BJY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DV4:4-{[4-(acetylamino)-1-methyl-1H-pyrrole-2-carbonyl]amino}-1-methyl-N-{4-[(1-methyl-1H-pyrrol-3-yl)amino]-4-oxobutyl}-1H-imidazole-2-carboxamide'>DV4</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2gic\|2gic]]</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=6bjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bjy OCA], [http://pdbe.org/6bjy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bjy RCSB], [http://www.ebi.ac.uk/pdbsum/6bjy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bjy ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NCAP_VSIVA NCAP_VSIVA]] Encapsidates the genome in a ratio of one N per nine ribonucleotides, protecting it from nucleases. The encapsidated genomic RNA is termed the NC and serves as template for transcription and replication. Replication is dependent on intracellular concentration of newly synthesized N, termed N(0), which corresponds to the protein not associated with RNA. In contrast, when associated with RNA, it is termed N. During replication, encapsidation by N(0) is coupled to RNA synthesis and all replicative products are resistant to nucleases (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Polyamides have been shown to bind double-stranded DNA by complementing the curvature of the minor groove and forming various hydrogen bonds with DNA. Several polyamide molecules have been found to have potent antiviral activities against papillomavirus, a double-stranded DNA virus. By analogy, we reason that polyamides may also interact with the structured RNA bound in the nucleocapsid of a negative strand RNA virus. Vesicular stomatitis virus (VSV) was selected as a prototype virus to test this possibility since its genomic RNA encaspsidated in the nucleocapsid forms a structure resembling one strand of an A-form RNA duplex. One polyamide molecule, UMSL1011, was found to inhibit infection of VSV. To confirm that the polyamide targeted the nucleocapsid, a nucleocapsid-like particle (NLP) was incubated with UMSL1011. The encapsidated RNA in the polyamide treated NLP was protected from thermo-release and digestion by RNase A. UMSL1011 also inhibits viral RNA synthesis in the intracellular activity assay for the viral RNA-dependent RNA polymerase. The crystal structure revealed that UMSL1011 binds the structured RNA in the nucleocapsid. The conclusion of our studies is that the RNA in the nucleocapsid is a viable antiviral target of polyamides. Since the RNA structure in the nucleocapsid is similar in all negative strand RNA viruses, polyamides may be optimized to target the specific RNA genome of a negative strand RNA virus, such as respiratory syncytial virus and Ebola virus.IMPORTANCE Negative strand RNA viruses (NSVs) include several life-threatening pathogens, such as rabies virus, respiratory syncytial virus, and Ebola virus. There are no effective antiviral drugs against these viruses. Polyamides offer an exceptional opportunity because they may be optimized to target each NSV. Our studies on vesicular stomatitis virus, a NSV, demonstrated that a polyamide molecule could specifically target the viral RNA in the nucleocapsid and inhibit viral growth. The target specificity of the polyamide molecule was proved by its inhibition of thermo-release and RNA nuclease digestion of the RNA bound in a model nucleocapsid, and a crystal structure of the polyamide inside the nucleocapsid. This encouraging observation provided the proof-of-concept rationale for designing polyamides as antiviral drugs against NSVs.

-	~~Authors:~~ Gumpper, ~~R.H.~~, ~~Luo~~, M.	+	A polyamide inhibits replication of vesicular stomatitis virus by targeting RNA in the nucleocapsid.,Gumpper RH, Li W, Castaneda CH, Scuderi MJ, Bashkin JK, Luo M J Virol. 2018 Feb 7. pii: JVI.00146-18. doi: 10.1128/JVI.00146-18. PMID:29437970<ref>PMID:29437970</ref>

-	~~Description: VSV Nucleocapsid with Polyamide Bound~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Gumpper, R.H]]	+	<div class="pdbe-citations 6bjy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gumpper, R H]]
	[[Category: Luo, M]]		[[Category: Luo, M]]
		+	[[Category: Nucleocapisd]]
		+	[[Category: Nucleocapsid-like particle]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Rna binding protein-rna complex]]
		+	[[Category: Vsv]]

OCA at 05:14, 15 February 2018

OCA — Thu, 15 Feb 2018 05:14:39 GMT

←Older revision		Revision as of 05:14, 15 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6bjy is ON HOLD	+	The entry 6bjy is ON HOLD until Paper Publication

	Authors: Gumpper, R.H., Luo, M.		Authors: Gumpper, R.H., Luo, M.

OCA at 05:05, 7 February 2018

OCA — Wed, 07 Feb 2018 05:05:40 GMT

←Older revision		Revision as of 05:05, 7 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6bjy is ON HOLD ~~until sometime in the future~~	+	The entry 6bjy is ON HOLD

	Authors: Gumpper, R.H., Luo, M.		Authors: Gumpper, R.H., Luo, M.

OCA at 05:50, 13 December 2017

OCA — Wed, 13 Dec 2017 05:50:39 GMT

←Older revision		Revision as of 05:50, 13 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6bjy is ON HOLD	+	The entry 6bjy is ON HOLD until sometime in the future

	Authors: Gumpper, R.H., Luo, M.		Authors: Gumpper, R.H., Luo, M.

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

OCA — Wed, 15 Nov 2017 06:23:51 GMT

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

←Older revision

Revision as of 06:23, 15 November 2017

OCA: New page: '''Unreleased structure''' The entry 6bjy is ON HOLD Authors: Gumpper, R.H., Luo, M. Description: VSV Nucleocapsid with Polyamide Bound Category: Unreleased Structures [[Category: ...

OCA — Wed, 15 Nov 2017 06:23:50 GMT

New page: '''Unreleased structure''' The entry 6bjy is ON HOLD Authors: Gumpper, R.H., Luo, M. Description: VSV Nucleocapsid with Polyamide Bound Category: Unreleased Structures [[Category: ...

New page

'''Unreleased structure'''

The entry 6bjy is ON HOLD

Authors: Gumpper, R.H., Luo, M.

Description: VSV Nucleocapsid with Polyamide Bound
[[Category: Unreleased Structures]]
[[Category: Gumpper, R.H]]
[[Category: Luo, M]]