3j9s

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<SX load='3j9s' size='340' side='right' viewer='molstar' caption='[[3j9s]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
<SX load='3j9s' size='340' side='right' viewer='molstar' caption='[[3j9s]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<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>
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<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>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
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<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>
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<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 ==
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[[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>
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[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>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3j9s" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
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__TOC__
</SX>
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[[Category: Bovine rotavirus strain UK/G6]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Grant, T]]
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[[Category: Grant T]]
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[[Category: Grigorieff, N]]
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[[Category: Grigorieff N]]
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[[Category: Rotavirus]]
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[[Category: Viral protein]]
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[[Category: Virus]]
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Revision as of 08:41, 7 February 2024

Single particle cryo-EM structure of rotavirus VP6 at 2.6 Angstrom resolution

3j9s, resolution 2.60Å

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