7L7K | pdb_00007l7k

Cryo-EM structure of protein encoded by vaccine candidate BNT162b2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7L7K

This is version 1.4 of the entry. See complete history

Literature

BNT162b vaccines protect rhesus macaques from SARS-CoV-2.

Vogel, A.B.Kanevsky, I.Che, Y.Swanson, K.A.Muik, A.Vormehr, M.Kranz, L.M.Walzer, K.C.Hein, S.Guler, A.Loschko, J.Maddur, M.S.Ota-Setlik, A.Tompkins, K.Cole, J.Lui, B.G.Ziegenhals, T.Plaschke, A.Eisel, D.Dany, S.C.Fesser, S.Erbar, S.Bates, F.Schneider, D.Jesionek, B.Sanger, B.Wallisch, A.K.Feuchter, Y.Junginger, H.Krumm, S.A.Heinen, A.P.Adams-Quack, P.Schlereth, J.Schille, S.Kroner, C.de la Caridad Guimil Garcia, R.Hiller, T.Fischer, L.Sellers, R.S.Choudhary, S.Gonzalez, O.Vascotto, F.Gutman, M.R.Fontenot, J.A.Hall-Ursone, S.Brasky, K.Griffor, M.C.Han, S.Su, A.A.H.Lees, J.A.Nedoma, N.L.Mashalidis, E.H.Sahasrabudhe, P.V.Tan, C.Y.Pavliakova, D.Singh, G.Fontes-Garfias, C.Pride, M.Scully, I.L.Ciolino, T.Obregon, J.Gazi, M.Carrion Jr., R.Alfson, K.J.Kalina, W.V.Kaushal, D.Shi, P.Y.Klamp, T.Rosenbaum, C.Kuhn, A.N.Tureci, O.Dormitzer, P.R.Jansen, K.U.Sahin, U.

(2021) Nature 592: 283-289

  • DOI: https://doi.org/10.1038/s41586-021-03275-y
  • Primary Citation Related Structures: 
    7L7F, 7L7K

  • PubMed Abstract: 

    A safe and effective vaccine against COVID-19 is urgently needed in quantities that are sufficient to immunize large populations. Here we report the preclinical development of two vaccine candidates (BNT162b1 and BNT162b2) that contain nucleoside-modified messenger RNA that encodes immunogens derived from the spike glycoprotein (S) of SARS-CoV-2, formulated in lipid nanoparticles. BNT162b1 encodes a soluble, secreted trimerized receptor-binding domain (known as the RBD-foldon). BNT162b2 encodes the full-length transmembrane S glycoprotein, locked in its prefusion conformation by the substitution of two residues with proline (S(K986P/V987P); hereafter, S(P2) (also known as P2 S)). The flexibly tethered RBDs of the RBD-foldon bind to human ACE2 with high avidity. Approximately 20% of the S(P2) trimers are in the two-RBD 'down', one-RBD 'up' state. In mice, one intramuscular dose of either candidate vaccine elicits a dose-dependent antibody response with high virus-entry inhibition titres and strong T-helper-1 CD4 + and IFNγ + CD8 + T cell responses. Prime-boost vaccination of rhesus macaques (Macaca mulatta) with the BNT162b candidates elicits SARS-CoV-2-neutralizing geometric mean titres that are 8.2-18.2× that of a panel of SARS-CoV-2-convalescent human sera. The vaccine candidates protect macaques against challenge with SARS-CoV-2; in particular, BNT162b2 protects the lower respiratory tract against the presence of viral RNA and shows no evidence of disease enhancement. Both candidates are being evaluated in phase I trials in Germany and the USA 1-3 , and BNT162b2 is being evaluated in an ongoing global phase II/III trial (NCT04380701 and NCT04368728).


  • Organizational Affiliation
    • BioNTech, Mainz, Germany.

Macromolecule Content 

  • Total Structure Weight: 423.79 kDa 
  • Atom Count: 22,124 
  • Modeled Residue Count: 2,919 
  • Deposited Residue Count: 3,819 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoproteinA [auth B],
B [auth C],
C [auth A]
1,273Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references
  • Version 1.2: 2021-04-21
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2025-05-14
    Changes: Data collection