7B3Y

Structure of a nanoparticle for a COVID-19 vaccine candidate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A COVID-19 vaccine candidate using SpyCatcher multimerization of the SARS-CoV-2 spike protein receptor-binding domain induces potent neutralising antibody responses.

Tan, T.K.Rijal, P.Rahikainen, R.Keeble, A.H.Schimanski, L.Hussain, S.Harvey, R.Hayes, J.W.P.Edwards, J.C.McLean, R.K.Martini, V.Pedrera, M.Thakur, N.Conceicao, C.Dietrich, I.Shelton, H.Ludi, A.Wilsden, G.Browning, C.Zagrajek, A.K.Bialy, D.Bhat, S.Stevenson-Leggett, P.Hollinghurst, P.Tully, M.Moffat, K.Chiu, C.Waters, R.Gray, A.Azhar, M.Mioulet, V.Newman, J.Asfor, A.S.Burman, A.Crossley, S.Hammond, J.A.Tchilian, E.Charleston, B.Bailey, D.Tuthill, T.J.Graham, S.P.Duyvesteyn, H.M.E.Malinauskas, T.Huo, J.Tree, J.A.Buttigieg, K.R.Owens, R.J.Carroll, M.W.Daniels, R.S.McCauley, J.W.Stuart, D.I.Huang, K.A.Howarth, M.Townsend, A.R.

(2021) Nat Commun 12: 542-542

  • DOI: https://doi.org/10.1038/s41467-020-20654-7
  • Primary Citation of Related Structures:  
    7B3Y

  • PubMed Abstract: 

    There is need for effective and affordable vaccines against SARS-CoV-2 to tackle the ongoing pandemic. In this study, we describe a protein nanoparticle vaccine against SARS-CoV-2. The vaccine is based on the display of coronavirus spike glycoprotein receptor-binding domain (RBD) on a synthetic virus-like particle (VLP) platform, SpyCatcher003-mi3, using SpyTag/SpyCatcher technology. Low doses of RBD-SpyVLP in a prime-boost regimen induce a strong neutralising antibody response in mice and pigs that is superior to convalescent human sera. We evaluate antibody quality using ACE2 blocking and neutralisation of cell infection by pseudovirus or wild-type SARS-CoV-2. Using competition assays with a monoclonal antibody panel, we show that RBD-SpyVLP induces a polyclonal antibody response that recognises key epitopes on the RBD, reducing the likelihood of selecting neutralisation-escape mutants. Moreover, RBD-SpyVLP is thermostable and can be lyophilised without losing immunogenicity, to facilitate global distribution and reduce cold-chain dependence. The data suggests that RBD-SpyVLP provides strong potential to address clinical and logistic challenges of the COVID-19 pandemic.


  • Organizational Affiliation

    MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK. tiong.tan@rdm.ox.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibronectin binding protein,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolaseA [auth B]341Streptococcus pyogenes NZ131Thermotoga maritima MSB8
This entity is chimeric
Mutation(s): 0 
Gene Names: prtFSpy49_0119TM_0066
UniProt
Find proteins for Q9WXS1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WXS1 
Go to UniProtKB:  Q9WXS1
Find proteins for A0A0H3BX48 (Streptococcus pyogenes serotype M49 (strain NZ131))
Explore A0A0H3BX48 
Go to UniProtKB:  A0A0H3BX48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0A0H3BX48Q9WXS1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.18.203874

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesUnited Kingdom2018-I2M-2-002

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references