Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G, A892P, A942P and V987P)(One up trimer)

Experimental Data Snapshot

  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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Stabilizing the closed SARS-CoV-2 spike trimer.

Juraszek, J.Rutten, L.Blokland, S.Bouchier, P.Voorzaat, R.Ritschel, T.Bakkers, M.J.G.Renault, L.L.R.Langedijk, J.P.M.

(2021) Nat Commun 12: 244-244

  • DOI: https://doi.org/10.1038/s41467-020-20321-x
  • Primary Citation of Related Structures:  
    7A4N, 7AD1

  • PubMed Abstract: 

    The trimeric spike (S) protein of SARS-CoV-2 is the primary focus of most vaccine design and development efforts. Due to intrinsic instability typical of class I fusion proteins, S tends to prematurely refold to the post-fusion conformation, compromising immunogenic properties and prefusion trimer yields. To support ongoing vaccine development efforts, we report the structure-based design of soluble S trimers with increased yields and stabilities, based on introduction of single point mutations and disulfide-bridges. We identify regions critical for stability: the heptad repeat region 1, the SD1 domain and position 614 in SD2. We combine a minimal selection of mostly interprotomeric mutations to create a stable S-closed variant with a 6.4-fold higher expression than the parental construct while no longer containing a heterologous trimerization domain. The cryo-EM structure reveals a correctly folded, predominantly closed pre-fusion conformation. Highly stable and well producing S protein and the increased understanding of S protein structure will support vaccine development and serological diagnostics.

  • Organizational Affiliation

    Janssen Vaccines & Prevention B.V., Archimedesweg 4-6, Leiden, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein,Envelope glycoprotein,Spike glycoprotein,Envelope glycoprotein,SARS-CoV-2 S protein
A, B, C
1,297Severe acute respiratory syndrome coronavirus 2Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: S2S gene
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Find proteins for M1E1E4 (Human immunodeficiency virus 1)
Explore M1E1E4 
Go to UniProtKB:  M1E1E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0DTC2M1E1E4
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
D [auth E],
E [auth F],
F [auth G],
G [auth H],
H [auth I],
D [auth E],
E [auth F],
F [auth G],
G [auth H],
H [auth I],
I [auth J],
J [auth K],
K [auth L],
L [auth M],
M [auth N]
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references