3J7M
Virus model of brome mosaic virus (first half data set)
Summary for 3J7M
| Entry DOI | 10.2210/pdb3j7m/pdb |
| Related | 3J7L 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 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: 25185801DOI: 10.1038/ncomms5808 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.8 Å) |
Structure validation
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