6ZP7
SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up open conformation)
Summary for 6ZP7
| Entry DOI | 10.2210/pdb6zp7/pdb |
| Related | 6ZOW |
| EMDB information | 11328 11337 |
| Descriptor | Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (8 entities in total) |
| Functional Keywords | spike, prefusion, flexibility, open, viral protein |
| Biological source | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) |
| Total number of polymer chains | 3 |
| Total formula weight | 445665.52 |
| Authors | Martinez, M.,Marabini, R.,Carazo, J.M. (deposition date: 2020-07-08, release date: 2020-07-29, Last modification date: 2024-11-13) |
| Primary citation | Melero, R.,Sorzano, C.O.S.,Foster, B.,Vilas, J.L.,Martinez, M.,Marabini, R.,Ramirez-Aportela, E.,Sanchez-Garcia, R.,Herreros, D.,Del Cano, L.,Losana, P.,Fonseca-Reyna, Y.C.,Conesa, P.,Wrapp, D.,Chacon, P.,McLellan, J.S.,Tagare, H.D.,Carazo, J.M. Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. Iucrj, 7:1059-1069, 2020 Cited by PubMed Abstract: Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been analysed. These studies revealed concerted motions involving the receptor-binding domain (RBD), N-terminal domain, and subdomains 1 and 2 around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. It is shown that in this data set there are not well defined, stable spike conformations, but virtually a continuum of states. An ensemble map was obtained with minimum bias, from which the extremes of the change along the direction of maximal variance were modeled by flexible fitting. The results provide a warning of the potential image-processing classification instability of these complicated data sets, which has a direct impact on the interpretability of the results. PubMed: 33063791DOI: 10.1107/S2052252520012725 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.3 Å) |
Structure validation
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