3J7L

Full virus map of brome mosaic virus

Summary for 3J7L

• Entry DOI: 10.2210/pdb3j7l/pdb
• Related: 3J7M 3J7N
• EMDB information: 6000
• Descriptor: Capsid protein (1 entity in total)
• Functional Keywords: capsid protein, bmv, beta barrel, virus
• Biological source: Brome mosaic virus (BMV)
• Total number of polymer chains: 3
• Total formula weight: 61234.58

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 citation

Wang, 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

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

Experimental method

ELECTRON MICROSCOPY (3.8 Å)