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TitleContinuous flexibility analysis of SARS-CoV-2 spike prefusion structures.
Journal, issue, pagesIUCrJ, Vol. 7, Issue Pt 6, Page 1059-1069, Year 2020
Publish dateSep 29, 2020
AuthorsRoberto Melero / Carlos Oscar S Sorzano / Brent Foster / José-Luis Vilas / Marta Martínez / Roberto Marabini / Erney Ramírez-Aportela / Ruben Sanchez-Garcia / David Herreros / Laura Del Caño / Patricia Losana / Yunior C Fonseca-Reyna / Pablo Conesa / Daniel Wrapp / Pablo Chacon / Jason S McLellan / Hemant D Tagare / Jose-Maria Carazo /
PubMed AbstractUsing 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 ...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.
External linksIUCrJ / PubMed:33063791 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 3.3 Å
Structure data

11328

6zow

EMDB-11328, PDB-6zow:
SARS-CoV-2 spike in prefusion state
Method: EM (single particle) / Resolution: 3.0 Å

11336

6zp5

EMDB-11336, PDB-6zp5:
SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up closed conformation)
Method: EM (single particle) / Resolution: 3.1 Å

11337

6zp7

EMDB-11337, PDB-6zp7:
SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up open conformation)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-11341:
SARS-CoV-2 stabilized spike in prefusion state (1-up conformation)
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-MAN:
alpha-D-mannopyranose / Mannose

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM / Dimethyl sulfoxide

ChemComp-HOH:
WATER / Water

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / Spike / Prefusion / Flexibility / Closed / Open

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