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3J7M

Virus model of brome mosaic virus (first half data set)

Summary for 3J7M
Entry DOI10.2210/pdb3j7m/pdb
Related3J7L 3J7N
EMDB information6000
DescriptorCapsid protein (1 entity in total)
Functional Keywordscapsid protein, bmv, beta barrel, virus
Biological sourceBrome mosaic virus (BMV)
Total number of polymer chains3
Total formula weight61234.58
Authors
Wang, Z.,Hryc, C.,Bammes, B.,Afonine, P.V.,Jakana, J.,Chen, D.H.,Liu, X.,Baker, M.L.,Kao, C.,Ludtke, S.J.,Schmid, M.F.,Adams, P.D.,Chiu, W. (deposition date: 2014-07-18, release date: 2014-09-10, Last modification date: 2024-02-21)
Primary citationWang, Z.,Hryc, C.F.,Bammes, B.,Afonine, P.V.,Jakana, J.,Chen, D.H.,Liu, X.,Baker, M.L.,Kao, C.,Ludtke, S.J.,Schmid, M.F.,Adams, P.D.,Chiu, W.
An atomic model of brome mosaic virus using direct electron detection and real-space optimization.
Nat Commun, 5:4808-4808, 2014
Cited by
PubMed Abstract: 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 Å 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.
PubMed: 25185801
DOI: 10.1038/ncomms5808
PDB entries with the same primary citation
Experimental method
ELECTRON MICROSCOPY (3.8 Å)
Structure validation

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