6y6k - Revision history

OCA at 10:20, 22 May 2024

2024-05-22T10:20:41Z

←Older revision		Revision as of 10:20, 22 May 2024
Line 3:		Line 3:
	<StructureSection load='6y6k' size='340' side='right'caption='[[6y6k]], [[Resolution\|resolution]] 3.78Å' scene=''>		<StructureSection load='6y6k' size='340' side='right'caption='[[6y6k]], [[Resolution\|resolution]] 3.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6y6k]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Phlebovirus_ah12/china/2010 Phlebovirus ah12/china/2010~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y6K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6Y6K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y6k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/SFTS_virus_AH12 SFTS virus AH12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y6K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y6K FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</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]] 3.78Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6xya\|6xya]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6y6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y6k OCA], [~~http~~://pdbe.org/6y6k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6y6k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6y6k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6y6k 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=6y6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y6k OCA], [https://pdbe.org/6y6k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y6k RCSB], [https://www.ebi.ac.uk/pdbsum/6y6k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y6k ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/L_SFTS L_SFTS]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Phlebovirus ah12/china/2010~~]]	+	[[Category: SFTS virus AH12]]
-	[[Category: Busch, C]]	+	[[Category: Busch C]]
-	[[Category: Cusack, S]]	+	[[Category: Cusack S]]
-	[[Category: Gogrefe, N]]	+	[[Category: Gogrefe N]]
-	[[Category: Gruenewald, K]]	+	[[Category: Gruenewald K]]
-	[[Category: Guenther, S]]	+	[[Category: Guenther S]]
-	[[Category: Kouba, T]]	+	[[Category: Kouba T]]
-	[[Category: Meier, K]]	+	[[Category: Meier K]]
-	[[Category: Quemin, E]]	+	[[Category: Quemin E]]
-	[[Category: Reindl, S]]	+	[[Category: Reindl S]]
-	[[Category: Rosenthal, M]]	+	[[Category: Rosenthal M]]
-	[[Category: Thorkelsson~~, S R~~]]	+	[[Category: Thorkelsson SR]]
-	[[Category: Vogel, D]]	+	[[Category: Vogel D]]
-	~~[[Category: Bunyavirus]]~~	+
-	~~[[Category: Cap-snatching]]~~	+
-	~~[[Category: L protein]]~~	+
-	~~[[Category: Phenuiviridae]]~~	+
-	~~[[Category: Viral polymerase]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 07:18, 29 April 2020

2020-04-29T07:18:01Z

←Older revision		Revision as of 07:18, 29 April 2020
Line 3:		Line 3:
	<StructureSection load='6y6k' size='340' side='right'caption='[[6y6k]], [[Resolution\|resolution]] 3.78Å' scene=''>		<StructureSection load='6y6k' size='340' side='right'caption='[[6y6k]], [[Resolution\|resolution]] 3.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6y6k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y6K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y6K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y6k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Phlebovirus_ah12/china/2010 Phlebovirus ah12/china/2010]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y6K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y6K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6xya\|6xya]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6xya\|6xya]]</td></tr>
Line 10:		Line 10:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite~~. The ~~use~~ of ~~a simplified refinement target function enables very fast calculation~~, ~~which in turn makes it possible to identify optimal data-restraint weights~~ as ~~part~~ of ~~routine refinements with little runtime cost~~. ~~Refinement~~ of ~~atomic models against low-resolution data benefits from~~ the ~~inclusion of as much additional information as~~ is ~~available. In addition to standard restraints on covalent geometry, phenix~~.~~real_space_refine makes use~~ of ~~extra information such as secondary~~-~~structure~~ and ~~rotamer~~-~~specific restraints~~, ~~as well as restraints or constraints on internal molecular symmetry~~. ~~The re~~-~~refinement~~ of ~~385~~ cryo-EM-~~derived~~ models ~~available~~ in the ~~Protein Data Bank at resolutions of 6 A or better shows significant improvement~~ of the ~~models~~ and of the ~~fit~~ of ~~these models to~~ the ~~target maps~~.	+	The Bunyavirales order contains several emerging viruses with high epidemic potential, including Severe fever with thrombocytopenia syndrome virus (SFTSV). The lack of medical countermeasures, such as vaccines and antivirals, is a limiting factor for the containment of any virus outbreak. To develop such antivirals a profound understanding of the viral replication process is essential. The L protein of bunyaviruses is a multi-functional and multi-domain protein performing both virus transcription and genome replication and, therefore, is an ideal drug target. We established expression and purification procedures for the full-length L protein of SFTSV. By combining single-particle electron cryo-microscopy and X-ray crystallography, we obtained 3D models covering approximately 70% of the SFTSV L protein in the apo-conformation including the polymerase core region, the endonuclease and the cap-binding domain. We compared this first L structure of the Phenuiviridae family to the structures of La Crosse peribunyavirus L protein and influenza orthomyxovirus polymerase. Together with a comprehensive biochemical characterization of the distinct functions of SFTSV L protein, this work provides a solid framework for future structural and functional studies of L protein-RNA interactions and the development of antiviral strategies against this group of emerging human pathogens.

-	~~Real-space refinement in PHENIX for cryo-EM~~ and ~~crystallography~~.,~~Afonine PV~~, ~~Poon BK~~, ~~Read RJ~~, ~~Sobolev OV~~, ~~Terwilliger TC~~, ~~Urzhumtsev A~~, ~~Adams PD Acta Crystallogr D Struct Biol~~. ~~2018 Jun 1;74(Pt 6)~~:~~531-544~~. doi:, 10.~~1107~~/~~S2059798318006551. Epub 2018 May 30~~. PMID:~~29872004~~<ref>PMID:~~29872004~~</ref>	+	Structural and functional characterization of the severe fever with thrombocytopenia syndrome virus L protein.,Vogel D, Thorkelsson SR, Quemin ERJ, Meier K, Kouba T, Gogrefe N, Busch C, Reindl S, Gunther S, Cusack S, Grunewald K, Rosenthal M Nucleic Acids Res. 2020 Apr 20. pii: 5822961. doi: 10.1093/nar/gkaa253. PMID:32313945<ref>PMID:32313945</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Phlebovirus ah12/china/2010]]
	[[Category: Busch, C]]		[[Category: Busch, C]]
	[[Category: Cusack, S]]		[[Category: Cusack, S]]

OCA at 07:03, 8 April 2020

2020-04-08T07:03:23Z

←Older revision		Revision as of 07:03, 8 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6y6k is ~~ON HOLD~~	+	==Cryo-EM structure of a Phenuiviridae L protein==
		+	<StructureSection load='6y6k' size='340' side='right'caption='[[6y6k]], [[Resolution\|resolution]] 3.78Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6y6k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y6K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y6K FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6xya\|6xya]]</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=6y6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y6k OCA], [http://pdbe.org/6y6k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y6k RCSB], [http://www.ebi.ac.uk/pdbsum/6y6k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y6k ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 A or better shows significant improvement of the models and of the fit of these models to the target maps.

-	~~Authors~~:	+	Real-space refinement in PHENIX for cryo-EM and crystallography.,Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):531-544. doi:, 10.1107/S2059798318006551. Epub 2018 May 30. PMID:29872004<ref>PMID:29872004</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6y6k" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Busch, C]]
		+	[[Category: Cusack, S]]
		+	[[Category: Gogrefe, N]]
		+	[[Category: Gruenewald, K]]
		+	[[Category: Guenther, S]]
		+	[[Category: Kouba, T]]
		+	[[Category: Meier, K]]
		+	[[Category: Quemin, E]]
		+	[[Category: Reindl, S]]
		+	[[Category: Rosenthal, M]]
		+	[[Category: Thorkelsson, S R]]
		+	[[Category: Vogel, D]]
		+	[[Category: Bunyavirus]]
		+	[[Category: Cap-snatching]]
		+	[[Category: L protein]]
		+	[[Category: Phenuiviridae]]
		+	[[Category: Viral polymerase]]
		+	[[Category: Viral protein]]

OCA: Protected "6y6k" [edit=sysop:move=sysop]

2020-03-04T05:47:07Z

Protected "6y6k" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:47, 4 March 2020

OCA: New page: '''Unreleased structure''' The entry 6y6k is ON HOLD Authors: Description: Category: Unreleased Structures

2020-03-04T05:47:06Z

New page: '''Unreleased structure''' The entry 6y6k is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6y6k is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]