6ZWV

Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: 3 Closed RBDs

• PDB DOI:  https://doi.org/10.2210/pdb6ZWV/pdb
• EM Map EMD-11497: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Mutation(s): No 


• Deposited: 2020-07-28 Released: 2020-08-05 
• Deposition Author(s): Ke, Z., Qu, K., Nakane, T., Xiong, X., Cortese, M., Zila, V., Scheres, S.H.W., Briggs, J.A.G.
• Funding Organization(s): European Research Council (ERC), Medical Research Council (MRC, United Kingdom), German Research Foundation (DFG), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures and distributions of SARS-CoV-2 spike proteins on intact virions.

Ke, Z., Oton, J., Qu, K., Cortese, M., Zila, V., McKeane, L., Nakane, T., Zivanov, J., Neufeldt, C.J., Cerikan, B., Lu, J.M., Peukes, J., Xiong, X., Krausslich, H.G., Scheres, S.H.W., Bartenschlager, R., Briggs, J.A.G.

(2020) Nature 588: 498-502

• PubMed: 32805734 
• DOI: https://doi.org/10.1038/s41586-020-2665-2
• Primary Citation of Related Structures:  
  6ZWV


• PubMed Abstract: 
  

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virions are surrounded by a lipid bilayer from which spike (S) protein trimers protrude ¹ . Heavily glycosylated S trimers bind to the angiotensin-converting enzyme 2 receptor and mediate entry of virions into target cells ^2-6 . S exhibits extensive conformational flexibility: it modulates exposure of its receptor-binding site and subsequently undergoes complete structural rearrangement to drive fusion of viral and cellular membranes ^2,7,8 . The structures and conformations of soluble, overexpressed, purified S proteins have been studied in detail using cryo-electron microscopy ^2,7,9-12 , but the structure and distribution of S on the virion surface remain unknown. Here we applied cryo-electron microscopy and tomography to image intact SARS-CoV-2 virions and determine the high-resolution structure, conformational flexibility and distribution of S trimers in situ on the virion surface. These results reveal the conformations of S on the virion, and provide a basis from which to understand interactions between S and neutralizing antibodies during infection or vaccination.

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Organizational Affiliation: 

Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 437.38 kDa 
• Atom Count: 24,015 
• Modelled Residue Count: 2,955 
• Deposited Residue Count: 3,819 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,273	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth F], E [auth Q], F [auth S], G [auth V], H [auth X], I [auth b], J [auth k], K [auth m], L [auth p], M [auth r], N [auth v], O [auth 4], P [auth 6], Q [auth 9], R [auth BA]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth A], BA [auth A], CA [auth A], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], OA [auth C], PA [auth C], QA [auth C], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth A], YA [auth C], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18.2
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Ke, Z., Qu, K., Nakane, T., Xiong, X., Cortese, M., Zila, V., Scheres, S.H.W., Briggs, J.A.G.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	ERC-CoG-648432
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_1201/16
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_A025_1013
German Research Foundation (DFG)	Germany	240245660-SFB 1129
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2020-08-26
  Changes: Database references
• Version 1.2: 2020-09-02
  Changes: Database references
• Version 1.3: 2020-12-30
  Changes: Database references