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- PDB-7b3y: Structure of a nanoparticle for a COVID-19 vaccine candidate -

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Basic information

Entry
Database: PDB / ID: 7b3y
TitleStructure of a nanoparticle for a COVID-19 vaccine candidate
ComponentsFibronectin binding protein,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
KeywordsVIRUS LIKE PARTICLE / SARS-CoV-2 / SpyTag / VLP / Receptor-binding domain / vaccine / COVID-19 / SpyCatcher / nanocage / icosahedral / nanoparticle / coronavirus / mi3
Function / homology
Function and homology information


cell wall / cell adhesion / lyase activity / extracellular region
Similarity search - Function
Fibronectin binding repeat / Collagen-binding surface protein Cna-like, B-type domain / Fibronectin binding repeat / Cna protein B-type domain / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / KDPG/KHG aldolase / SDR-like Ig domain / KDPG and KHG aldolase / Bacterial Ig domain ...Fibronectin binding repeat / Collagen-binding surface protein Cna-like, B-type domain / Fibronectin binding repeat / Cna protein B-type domain / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / KDPG/KHG aldolase / SDR-like Ig domain / KDPG and KHG aldolase / Bacterial Ig domain / Fibrogen-binding domain 1 / Prealbumin-like fold domain / Prealbumin-like fold domain / Adhesion domain superfamily / Aldolase-type TIM barrel / Immunoglobulin-like fold
Similarity search - Domain/homology
Fibronectin binding protein / 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M49 (bacteria)
Thermotoga maritima (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDuyvesteyn, H.M.E. / Stuart, D.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences2018-I2M-2-002 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: A COVID-19 vaccine candidate using SpyCatcher multimerization of the SARS-CoV-2 spike protein receptor-binding domain induces potent neutralising antibody responses.
Authors: Tiong Kit Tan / Pramila Rijal / Rolle Rahikainen / Anthony H Keeble / Lisa Schimanski / Saira Hussain / Ruth Harvey / Jack W P Hayes / Jane C Edwards / Rebecca K McLean / Veronica Martini / ...Authors: Tiong Kit Tan / Pramila Rijal / Rolle Rahikainen / Anthony H Keeble / Lisa Schimanski / Saira Hussain / Ruth Harvey / Jack W P Hayes / Jane C Edwards / Rebecca K McLean / Veronica Martini / Miriam Pedrera / Nazia Thakur / Carina Conceicao / Isabelle Dietrich / Holly Shelton / Anna Ludi / Ginette Wilsden / Clare Browning / Adrian K Zagrajek / Dagmara Bialy / Sushant Bhat / Phoebe Stevenson-Leggett / Philippa Hollinghurst / Matthew Tully / Katy Moffat / Chris Chiu / Ryan Waters / Ashley Gray / Mehreen Azhar / Valerie Mioulet / Joseph Newman / Amin S Asfor / Alison Burman / Sylvia Crossley / John A Hammond / Elma Tchilian / Bryan Charleston / Dalan Bailey / Tobias J Tuthill / Simon P Graham / Helen M E Duyvesteyn / Tomas Malinauskas / Jiandong Huo / Julia A Tree / Karen R Buttigieg / Raymond J Owens / Miles W Carroll / Rodney S Daniels / John W McCauley / David I Stuart / Kuan-Ying A Huang / Mark Howarth / Alain R Townsend /
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 ...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.
History
DepositionDec 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Assembly

Deposited unit
B: Fibronectin binding protein,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase


Theoretical massNumber of molelcules
Total (without water)36,0011
Polymers36,0011
Non-polymers00
Water00
1
B: Fibronectin binding protein,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
x 60


Theoretical massNumber of molelcules
Total (without water)2,160,04360
Polymers2,160,04360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation59

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Components

#1: Protein Fibronectin binding protein,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase


Mass: 36000.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Model just contains mi3 cage component of VLP. Note that the Spy and RBD (spy tag and RBD are omitted from the sequence) are are not included in the model. The spycatcher003-mi3 can be found ...Details: Model just contains mi3 cage component of VLP. Note that the Spy and RBD (spy tag and RBD are omitted from the sequence) are are not included in the model. The spycatcher003-mi3 can be found on genbank with code MT945417 and that of the SpyTag-RBD at MT945427.,Model just contains mi3 cage component of VLP. Note that the Spy and RBD (spy tag and RBD are omitted from the sequence) are are not included in the model. The spycatcher003-mi3 can be found on genbank with code MT945417 and that of the SpyTag-RBD at MT945427.
Source: (gene. exp.) Streptococcus pyogenes serotype M49 (strain NZ131) (bacteria), (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: NZ131, ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: prtF, Spy49_0119, TM_0066 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3BX48, UniProt: Q9WXS1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RBD-Spycatcher-mi3 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: PBS
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Calibrated magnification: 165000 X / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48.1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7393
Details: SerialEM collection employing beam tilt for multishots per hole using custom script.
EM imaging opticsEnergyfilter slit width: 30 eV
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARCparticle selection
2SerialEM3.8.0image acquisitionbeta
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
8Coot0.9.2model fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
20PHENIX1.18.203874model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150785 / Symmetry type: POINT
Atomic model buildingB value: 9.4 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 5KP9

5kp9

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