3j9s - Revision history

OCA at 08:41, 7 February 2024

OCA — Wed, 07 Feb 2024 08:41:35 GMT

←Older revision		Revision as of 08:41, 7 February 2024
Line 3:		Line 3:
	<SX load='3j9s' size='340' side='right' viewer='molstar' caption='[[3j9s]], [[Resolution\|resolution]] 2.60Å' scene=''>		<SX load='3j9s' size='340' side='right' viewer='molstar' caption='[[3j9s]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j9s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bovine_rotavirus_(strain_uk)~~ Bovine rotavirus (strain ~~uk)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J9S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j9s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bovine_rotavirus_strain_UK/G6 Bovine rotavirus strain UK/G6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J9S FirstGlance]. <br>
-	</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>~~, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.6Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3j9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9s OCA], [https://pdbe.org/3j9s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j9s RCSB], [https://www.ebi.ac.uk/pdbsum/3j9s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j9s 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=3j9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9s OCA], [https://pdbe.org/3j9s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j9s RCSB], [https://www.ebi.ac.uk/pdbsum/3j9s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j9s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~VP6_ROTRF VP6_ROTRF]~~] Intermediate capsid protein that self assembles to form an icosahedral capsid with a T=13 symmetry, which consists of 230 trimers of VP6, with channels at each of its five-fold vertices. This capsid constitutes the middle concentric layer of the viral mature particle. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. ~~Nacent~~ transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels at the five-fold axes. VP6 is required for the transcription activity of the DLP.~~<ref>PMID:6292454</ref>~~	+	[https://www.uniprot.org/uniprot/VP6_ROTBU VP6_ROTBU] Intermediate capsid protein that self assembles to form an icosahedral capsid with a T=13 symmetry, which consists of 230 trimers of VP6, with channels at each of its five-fold vertices (PubMed:20122940). This capsid constitutes the middle concentric layer of the viral mature particle (PubMed:20122940). The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus (By similarity). Nascent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels at the five-fold axes (PubMed:20122940). VP6 is required for the transcription activity of the DLP (By similarity).[HAMAP-Rule:MF_04129]<ref>PMID:20122940</ref>
-	~~<div style="background~~-~~color~~:~~#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Biological specimens suffer radiation damage when imaged in an electron microscope, ultimately limiting the attainable resolution. At a given resolution, an optimal exposure can be defined that maximizes the signal-to-noise ratio in the image. Using a 2.6 A resolution single particle cryo-EM reconstruction of rotavirus VP6, determined from movies recorded with a total exposure of 100 electrons/A2, we obtained accurate measurements of optimal exposure values over a wide range of resolutions. At low and intermediate resolutions our measured values are considerably higher than obtained previously for crystalline specimens, indicating that both images and movies should be collected with higher exposures than are generally used. We demonstrate a method of using our optimal exposure values to filter movie frames, yielding images with improved contrast that lead to higher resolution reconstructions. This 'high-exposure' technique should benefit cryo-EM work on all types of samples, especially those of relatively low molecular mass.	+
-		+
-	~~Measuring the optimal exposure for single particle cryo-EM using a 2.6 A reconstruction of rotavirus VP6.,Grant T, Grigorieff N Elife. 2015 May 29;4. doi: 10.7554/eLife.06980. PMID:26023829~~<ref>PMID:~~26023829~~</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3j9s" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</SX>		</SX>
		+	[[Category: Bovine rotavirus strain UK/G6]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Grant, T]]	+	[[Category: Grant T]]
-	[[Category: Grigorieff, N]]	+	[[Category: Grigorieff N]]
-	~~[[Category: Rotavirus]]~~	+
-	~~[[Category: Viral protein]]~~	+
-	~~[[Category: Virus~~]]	+

OCA at 13:29, 4 May 2022

OCA — Wed, 04 May 2022 13:29:08 GMT

←Older revision		Revision as of 13:29, 4 May 2022
Line 3:		Line 3:
	<SX load='3j9s' size='340' side='right' viewer='molstar' caption='[[3j9s]], [[Resolution\|resolution]] 2.60Å' scene=''>		<SX load='3j9s' size='340' side='right' viewer='molstar' caption='[[3j9s]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j9s]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bovine_rotavirus_(strain_uk) Bovine rotavirus (strain uk)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3J9S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j9s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bovine_rotavirus_(strain_uk) Bovine rotavirus (strain uk)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J9S FirstGlance]. <br>
	</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>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</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>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</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=3j9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9s OCA], [~~http~~://pdbe.org/3j9s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3j9s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3j9s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3j9s 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=3j9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9s OCA], [https://pdbe.org/3j9s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j9s RCSB], [https://www.ebi.ac.uk/pdbsum/3j9s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j9s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VP6_ROTRF VP6_ROTRF]] Intermediate capsid protein that self assembles to form an icosahedral capsid with a T=13 symmetry, which consists of 230 trimers of VP6, with channels at each of its five-fold vertices. This capsid constitutes the middle concentric layer of the viral mature particle. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nacent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels at the five-fold axes. VP6 is required for the transcription activity of the DLP.<ref>PMID:6292454</ref>	+	[[https://www.uniprot.org/uniprot/VP6_ROTRF VP6_ROTRF]] Intermediate capsid protein that self assembles to form an icosahedral capsid with a T=13 symmetry, which consists of 230 trimers of VP6, with channels at each of its five-fold vertices. This capsid constitutes the middle concentric layer of the viral mature particle. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nacent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels at the five-fold axes. VP6 is required for the transcription activity of the DLP.<ref>PMID:6292454</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 18:15, 10 April 2020

OCA — Fri, 10 Apr 2020 18:15:53 GMT

←Older revision		Revision as of 18:15, 10 April 2020
Line 3:		Line 3:
	<SX load='3j9s' size='340' side='right' viewer='molstar' caption='[[3j9s]], [[Resolution\|resolution]] 2.60Å' scene=''>		<SX load='3j9s' size='340' side='right' viewer='molstar' caption='[[3j9s]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j9s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus_(strain_uk) Bovine rotavirus (strain uk)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9S OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3J9S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j9s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus_(strain_uk) Bovine rotavirus (strain uk)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9S OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3J9S 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>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</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>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</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=3j9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9s OCA], [http://pdbe.org/3j9s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j9s RCSB], [http://www.ebi.ac.uk/pdbsum/3j9s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j9s 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=3j9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9s OCA], [http://pdbe.org/3j9s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j9s RCSB], [http://www.ebi.ac.uk/pdbsum/3j9s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j9s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 17:32, 6 March 2020

OCA — Fri, 06 Mar 2020 17:32:58 GMT

←Older revision		Revision as of 17:32, 6 March 2020
Line 1:		Line 1:

	==Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution==		==Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution==
-	<~~StructureSection~~ load='3j9s' size='340' side='right' caption='[[3j9s]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<SX load='3j9s' size='340' side='right' viewer='molstar' caption='[[3j9s]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3j9s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus_(strain_uk) Bovine rotavirus (strain uk)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J9S FirstGlance]. <br>		<table><tr><td colspan='2'>[[3j9s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus_(strain_uk) Bovine rotavirus (strain uk)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J9S FirstGlance]. <br>
Line 22:		Line 22:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
		+	[[Category: Large Structures]]
	[[Category: Grant, T]]		[[Category: Grant, T]]
	[[Category: Grigorieff, N]]		[[Category: Grigorieff, N]]

OCA at 08:19, 18 July 2018

OCA — Wed, 18 Jul 2018 08:19:39 GMT

←Older revision		Revision as of 08:19, 18 July 2018
Line 1:		Line 1:
		+
	==Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution==		==Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution==
	<StructureSection load='3j9s' size='340' side='right' caption='[[3j9s]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3j9s' size='340' side='right' caption='[[3j9s]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j9s]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J9S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j9s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovine_rotavirus_(strain_uk) Bovine rotavirus (strain uk)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J9S 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>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</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=3j9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j9s RCSB], [http://www.ebi.ac.uk/pdbsum/3j9s PDBsum]</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=3j9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9s OCA], [http://pdbe.org/3j9s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j9s RCSB], [http://www.ebi.ac.uk/pdbsum/3j9s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j9s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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>
	</div>		</div>
		+	<div class="pdbe-citations 3j9s" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:44, 10 June 2015

OCA — Wed, 10 Jun 2015 07:44:58 GMT

←Older revision		Revision as of 07:44, 10 June 2015
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/VP6_ROTRF VP6_ROTRF]] Intermediate capsid protein that self assembles to form an icosahedral capsid with a T=13 symmetry, which consists of 230 trimers of VP6, with channels at each of its five-fold vertices. This capsid constitutes the middle concentric layer of the viral mature particle. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nacent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels at the five-fold axes. VP6 is required for the transcription activity of the DLP.<ref>PMID:6292454</ref>		[[http://www.uniprot.org/uniprot/VP6_ROTRF VP6_ROTRF]] Intermediate capsid protein that self assembles to form an icosahedral capsid with a T=13 symmetry, which consists of 230 trimers of VP6, with channels at each of its five-fold vertices. This capsid constitutes the middle concentric layer of the viral mature particle. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nacent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels at the five-fold axes. VP6 is required for the transcription activity of the DLP.<ref>PMID:6292454</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Biological specimens suffer radiation damage when imaged in an electron microscope, ultimately limiting the attainable resolution. At a given resolution, an optimal exposure can be defined that maximizes the signal-to-noise ratio in the image. Using a 2.6 A resolution single particle cryo-EM reconstruction of rotavirus VP6, determined from movies recorded with a total exposure of 100 electrons/A2, we obtained accurate measurements of optimal exposure values over a wide range of resolutions. At low and intermediate resolutions our measured values are considerably higher than obtained previously for crystalline specimens, indicating that both images and movies should be collected with higher exposures than are generally used. We demonstrate a method of using our optimal exposure values to filter movie frames, yielding images with improved contrast that lead to higher resolution reconstructions. This 'high-exposure' technique should benefit cryo-EM work on all types of samples, especially those of relatively low molecular mass.
		+
		+	Measuring the optimal exposure for single particle cryo-EM using a 2.6 A reconstruction of rotavirus VP6.,Grant T, Grigorieff N Elife. 2015 May 29;4. doi: 10.7554/eLife.06980. PMID:26023829<ref>PMID:26023829</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:52, 11 March 2015

OCA — Wed, 11 Mar 2015 11:52:45 GMT

←Older revision		Revision as of 11:52, 11 March 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution==
-		+	<StructureSection load='3j9s' size='340' side='right' caption='[[3j9s]], [[Resolution\|resolution]] 2.60Å' scene=''>
-	~~The entry~~ 3j9s is ~~ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3j9s]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J9S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J9S FirstGlance]. <br>
-	~~Authors~~: ~~Grant~~, T., ~~Grigorieff~~, N.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
-	~~Description~~: ~~Single particle cryo~~-~~EM structure~~ of ~~rotavirus~~ VP6 at 2.~~6 Angstrom resolution~~	+	<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=3j9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j9s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j9s RCSB], [http://www.ebi.ac.uk/pdbsum/3j9s PDBsum]</span></td></tr>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VP6_ROTRF VP6_ROTRF]] Intermediate capsid protein that self assembles to form an icosahedral capsid with a T=13 symmetry, which consists of 230 trimers of VP6, with channels at each of its five-fold vertices. This capsid constitutes the middle concentric layer of the viral mature particle. The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nacent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels at the five-fold axes. VP6 is required for the transcription activity of the DLP.<ref>PMID:6292454</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Grant, T]]		[[Category: Grant, T]]
	[[Category: Grigorieff, N]]		[[Category: Grigorieff, N]]
		+	[[Category: Rotavirus]]
		+	[[Category: Viral protein]]
		+	[[Category: Virus]]

OCA at 06:27, 4 March 2015

OCA — Wed, 04 Mar 2015 06:27:46 GMT

←Older revision		Revision as of 06:27, 4 March 2015
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	The entry 3j9s is ON HOLD		The entry 3j9s is ON HOLD

-	Authors: Grant, T, Grigorieff, N	+	Authors: Grant, T., Grigorieff, N.

-	Description: Single particle cryo-EM structure of rotavirus VP6 at 2.6 ~~Angstroms~~ resolution.	+	Description: Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Grant, T, Grigorieff, N]]	+	[[Category: Grant, T]]
		+	[[Category: Grigorieff, N]]

OCA: Protected "3j9s" [edit=sysop:move=sysop]

OCA — Wed, 25 Feb 2015 08:44:58 GMT

Protected "3j9s" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:44, 25 February 2015

OCA: New page: '''Unreleased structure''' The entry 3j9s is ON HOLD Authors: Grant, T, Grigorieff, N Description: Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstroms resolution. [[Cat...

OCA — Wed, 25 Feb 2015 08:44:57 GMT

New page: '''Unreleased structure''' The entry 3j9s is ON HOLD Authors: Grant, T, Grigorieff, N Description: Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstroms resolution. [[Cat...

New page

'''Unreleased structure'''

The entry 3j9s is ON HOLD

Authors: Grant, T, Grigorieff, N

Description: Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstroms resolution.
[[Category: Unreleased Structures]]
[[Category: Grant, T, Grigorieff, N]]