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==Virus model of brome mosaic virus (first half data set)==
==Virus model of brome mosaic virus (first half data set)==
<StructureSection load='3j7m' size='340' side='right' caption='[[3j7m]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
<SX load='3j7m' size='340' side='right' viewer='molstar' caption='[[3j7m]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3j7m]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Brome_mosaic_virus Brome mosaic virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J7M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J7M FirstGlance]. <br>
<table><tr><td colspan='2'>[[3j7m]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Brome_mosaic_virus Brome mosaic virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J7M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J7M FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3j7l|3j7l]], [[3j7n|3j7n]]</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]] 3.8&#8491;</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=3j7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j7m OCA], [http://pdbe.org/3j7m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j7m RCSB], [http://www.ebi.ac.uk/pdbsum/3j7m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j7m 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=3j7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j7m OCA], [https://pdbe.org/3j7m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j7m RCSB], [https://www.ebi.ac.uk/pdbsum/3j7m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j7m ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/CAPSD_BMV CAPSD_BMV]] Capsid protein. Binds specifically to the subgenomic RNA4 to ensure selective packaging.  
[https://www.uniprot.org/uniprot/CAPSD_BMV CAPSD_BMV] Capsid protein. Binds specifically to the subgenomic RNA4 to ensure selective packaging.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 A as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.
 
An atomic model of brome mosaic virus using direct electron detection and real-space optimization.,Wang Z, Hryc CF, Bammes B, Afonine PV, Jakana J, Chen DH, Liu X, Baker ML, Kao C, Ludtke SJ, Schmid MF, Adams PD, Chiu W Nat Commun. 2014 Sep 4;5:4808. doi: 10.1038/ncomms5808. PMID:25185801<ref>PMID:25185801</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3j7m" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Virus coat protein|Virus coat protein]]
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</SX>
[[Category: Brome mosaic virus]]
[[Category: Brome mosaic virus]]
[[Category: Adams, P D]]
[[Category: Large Structures]]
[[Category: Afonine, P V]]
[[Category: Adams PD]]
[[Category: Baker, M L]]
[[Category: Afonine PV]]
[[Category: Bammes, B]]
[[Category: Baker ML]]
[[Category: Chen, D H]]
[[Category: Bammes B]]
[[Category: Chiu, W]]
[[Category: Chen DH]]
[[Category: Hryc, C]]
[[Category: Chiu W]]
[[Category: Jakana, J]]
[[Category: Hryc C]]
[[Category: Kao, C]]
[[Category: Jakana J]]
[[Category: Liu, X]]
[[Category: Kao C]]
[[Category: Ludtke, S J]]
[[Category: Liu X]]
[[Category: Schmid, M F]]
[[Category: Ludtke SJ]]
[[Category: Wang, Z]]
[[Category: Schmid MF]]
[[Category: Beta barrel]]
[[Category: Wang Z]]
[[Category: Bmv]]
[[Category: Capsid protein]]
[[Category: Virus]]
Retrieved from "https://proteopedia.org/3j7m"