3j7m: Difference between revisions

<StructureSection load='3j7m' size='340' side='right' caption='[[3j7m]], [[Resolution|resolution]] 3.80&Aring;' scene=''>

<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>

</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3j7l|3j7l]], [[3j7n|3j7n]]</td></tr>

<tr><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://www.rcsb.org/pdb/explore.do?structureId=3j7m RCSB], [http://www.ebi.ac.uk/pdbsum/3j7m PDBsum]</span></td></tr>

<table>

<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>

== References ==

</StructureSection>

[[Category: Adams, P D.]]

[[Category: Afonine, P V.]]

[[Category: Baker, M L.]]

[[Category: Bammes, B.]]

[[Category: Chen, D H.]]

[[Category: Chiu, W.]]

[[Category: Hryc, C.]]

[[Category: Jakana, J.]]

[[Category: Kao, C.]]

[[Category: Liu, X.]]

[[Category: Ludtke, S J.]]

[[Category: Schmid, M F.]]

[[Category: Wang, Z.]]

[[Category: Virus]]