6yfi - Revision history

OCA at 07:39, 1 May 2024

OCA — Wed, 01 May 2024 07:39:59 GMT

←Older revision		Revision as of 07:39, 1 May 2024
Line 3:		Line 3:
	<StructureSection load='6yfi' size='340' side='right'caption='[[6yfi]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='6yfi' size='340' side='right'caption='[[6yfi]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yfi]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Leviviridae_sp. Leviviridae sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YFI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YFI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yfi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Leviviridae_sp. Leviviridae sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YFI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YFI FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>[[6yf7\|6yf7]]~~, [[~~6yf9~~\|6yf9]], [[6yfa\|6yfa]], [[6yfb\|6yfb]], [[6yfc\|6yfc]], [[6yfd\|6yfd]], [[6yfe\|6yfe]], [[6yff\|6yff]], [[6yfg\|6yfg]], [[6yfh\|6yfh]], [[6yfj\|6yfj]], [[6yfk\|6yfk]], [[6yfl\|6yfl]], [[6yfm\|6yfm]], [[6yfn\|6yfn]], [[6yfo\|6yfo]], [[6yfp\|6yfp]], [[6yfq\|6yfq]], [[6yfr\|6yfr]], [[6yfs\|6yfs]], [[6yft\|6yft]], [[6yfu\|6yfu]]~~</div>~~</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]] 1.248Å</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=6yfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yfi OCA], [~~http~~://pdbe.org/6yfi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6yfi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6yfi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6yfi 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=6yfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yfi OCA], [https://pdbe.org/6yfi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yfi RCSB], [https://www.ebi.ac.uk/pdbsum/6yfi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yfi ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The single-stranded RNA (ssRNA) bacteriophages are among the simplest known viruses with small genomes and exceptionally high mutation rates. The number of ssRNA phage isolates has remained very low, but recent metagenomic studies have uncovered an immense variety of distinct uncultured ssRNA phages. The coat proteins (CPs) in these genomes are particularly diverse, with notable variation in length and often no recognizable similarity to previously known viruses. We recombinantly expressed metagenome-derived ssRNA phage CPs to produce virus-like particles and determined the three-dimensional structure of 22 previously uncharacterized ssRNA phage capsids covering nine distinct CP types. The structures revealed substantial deviations from the previously known ssRNA phage CP fold, uncovered an unusual prolate particle shape, and revealed a previously unseen dsRNA binding mode. These data expand our knowledge of the evolution of viral structural proteins and are of relevance for applications such as ssRNA phage-based vaccine design.
-
-	Three-dimensional structure of 22 uncultured ssRNA bacteriophages: Flexibility of the coat protein fold and variations in particle shapes.,Rumnieks J, Lieknina I, Kalnins G, Sisovs M, Akopjana I, Bogans J, Tars K Sci Adv. 2020 Sep 2;6(36). pii: 6/36/eabc0023. doi: 10.1126/sciadv.abc0023. Print, 2020 Sep. PMID:32917600<ref>PMID:32917600</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6yfi" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Leviviridae sp]]		[[Category: Leviviridae sp]]
-	[[Category: Kalnins, G]]	+	[[Category: Kalnins G]]
-	[[Category: Lieknina, I]]	+	[[Category: Lieknina I]]
-	[[Category: Rumnieks, J]]	+	[[Category: Rumnieks J]]
-	[[Category: Sisovs, M]]	+	[[Category: Sisovs M]]
-	[[Category: Tars, K]]	+	[[Category: Tars K]]
-	~~[[Category: Structural protein]]~~	+
-	~~[[Category: Viral protein]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 12:55, 16 December 2020

OCA — Wed, 16 Dec 2020 12:55:14 GMT

←Older revision		Revision as of 12:55, 16 December 2020
Line 1:		Line 1:

	==Bacteriophage EMS014 coat protein==		==Bacteriophage EMS014 coat protein==
-	<StructureSection load='6yfi' size='340' side='right'caption='[[6yfi]]' scene=''>	+	<StructureSection load='6yfi' size='340' side='right'caption='[[6yfi]], [[Resolution\|resolution]] 1.25Å' 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=6YFI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YFI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yfi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Leviviridae_sp. Leviviridae sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YFI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YFI 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=6yfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yfi OCA], [http://pdbe.org/6yfi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yfi RCSB], [http://www.ebi.ac.uk/pdbsum/6yfi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yfi ProSAT]</span></td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6yf7\|6yf7]], [[6yf9\|6yf9]], [[6yfa\|6yfa]], [[6yfb\|6yfb]], [[6yfc\|6yfc]], [[6yfd\|6yfd]], [[6yfe\|6yfe]], [[6yff\|6yff]], [[6yfg\|6yfg]], [[6yfh\|6yfh]], [[6yfj\|6yfj]], [[6yfk\|6yfk]], [[6yfl\|6yfl]], [[6yfm\|6yfm]], [[6yfn\|6yfn]], [[6yfo\|6yfo]], [[6yfp\|6yfp]], [[6yfq\|6yfq]], [[6yfr\|6yfr]], [[6yfs\|6yfs]], [[6yft\|6yft]], [[6yfu\|6yfu]]</div></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=6yfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yfi OCA], [http://pdbe.org/6yfi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yfi RCSB], [http://www.ebi.ac.uk/pdbsum/6yfi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yfi ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The single-stranded RNA (ssRNA) bacteriophages are among the simplest known viruses with small genomes and exceptionally high mutation rates. The number of ssRNA phage isolates has remained very low, but recent metagenomic studies have uncovered an immense variety of distinct uncultured ssRNA phages. The coat proteins (CPs) in these genomes are particularly diverse, with notable variation in length and often no recognizable similarity to previously known viruses. We recombinantly expressed metagenome-derived ssRNA phage CPs to produce virus-like particles and determined the three-dimensional structure of 22 previously uncharacterized ssRNA phage capsids covering nine distinct CP types. The structures revealed substantial deviations from the previously known ssRNA phage CP fold, uncovered an unusual prolate particle shape, and revealed a previously unseen dsRNA binding mode. These data expand our knowledge of the evolution of viral structural proteins and are of relevance for applications such as ssRNA phage-based vaccine design.
		+
		+	Three-dimensional structure of 22 uncultured ssRNA bacteriophages: Flexibility of the coat protein fold and variations in particle shapes.,Rumnieks J, Lieknina I, Kalnins G, Sisovs M, Akopjana I, Bogans J, Tars K Sci Adv. 2020 Sep 2;6(36). pii: 6/36/eabc0023. doi: 10.1126/sciadv.abc0023. Print, 2020 Sep. PMID:32917600<ref>PMID:32917600</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yfi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kalnins G]]	+	[[Category: Leviviridae sp]]
-	[[Category: Lieknina I]]	+	[[Category: Kalnins, G]]
-	[[Category: Rumnieks J]]	+	[[Category: Lieknina, I]]
-	[[Category: Sisovs M]]	+	[[Category: Rumnieks, J]]
-	[[Category: Tars K]]	+	[[Category: Sisovs, M]]
		+	[[Category: Tars, K]]
		+	[[Category: Structural protein]]
		+	[[Category: Viral protein]]
		+	[[Category: Virus]]

OCA at 06:52, 2 September 2020

OCA — Wed, 02 Sep 2020 06:52:35 GMT

←Older revision		Revision as of 06:52, 2 September 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6yfi ~~is ON HOLD until Paper Publication~~	+	==Bacteriophage EMS014 coat protein==
-		+	<StructureSection load='6yfi' size='340' side='right'caption='[[6yfi]]' scene=''>
-	~~Authors~~: ~~Rumnieks, J~~., ~~Kalnins~~, G., ~~Sisovs, M~~., ~~Lieknina, I~~., ~~Tars, K~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YFI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YFI FirstGlance]. <br>
-	~~Description: Bacteriophage EMS014 coat protein~~	+	</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=6yfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yfi OCA], [http://pdbe.org/6yfi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yfi RCSB], [http://www.ebi.ac.uk/pdbsum/6yfi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yfi ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Lieknina, I~~]]	+	__TOC__
-	[[Category: ~~Kalnins, G~~]]	+	</StructureSection>
-	[[Category: Rumnieks, J]]	+	[[Category: Large Structures]]
-	[[Category: Sisovs, M]]	+	[[Category: Kalnins G]]
-	[[Category: Tars, K]]	+	[[Category: Lieknina I]]
		+	[[Category: Rumnieks J]]
		+	[[Category: Sisovs M]]
		+	[[Category: Tars K]]

OCA at 07:21, 22 July 2020

OCA — Wed, 22 Jul 2020 07:21:23 GMT

←Older revision		Revision as of 07:21, 22 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Rumnieks, J., Kalnins, G., Sisovs, M., Lieknina, I., Tars, K.		Authors: Rumnieks, J., Kalnins, G., Sisovs, M., Lieknina, I., Tars, K.

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

OCA — Wed, 01 Apr 2020 07:48:11 GMT

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

←Older revision

Revision as of 07:48, 1 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yfi is ON HOLD Authors: Rumnieks, J., Kalnins, G., Sisovs, M., Lieknina, I., Tars, K. Description: Bacteriophage EMS014 coat protein [[Category: U...

OCA — Wed, 01 Apr 2020 07:48:09 GMT

New page: '''Unreleased structure''' The entry 6yfi is ON HOLD Authors: Rumnieks, J., Kalnins, G., Sisovs, M., Lieknina, I., Tars, K. Description: Bacteriophage EMS014 coat protein [[Category: U...

New page

'''Unreleased structure'''

The entry 6yfi is ON HOLD

Authors: Rumnieks, J., Kalnins, G., Sisovs, M., Lieknina, I., Tars, K.

Description: Bacteriophage EMS014 coat protein
[[Category: Unreleased Structures]]
[[Category: Lieknina, I]]
[[Category: Kalnins, G]]
[[Category: Rumnieks, J]]
[[Category: Sisovs, M]]
[[Category: Tars, K]]