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- EMDB-11997: Structure of a nanoparticle for a COVID-19 vaccine candidate -

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Basic information

Entry
Database: EMDB / ID: EMD-11997
TitleStructure of a nanoparticle for a COVID-19 vaccine candidate
Map dataRBD Spy mi3 cage vlp
Sample
  • Complex: RBD-Spycatcher-mi3
    • Protein or peptide: Fibronectin binding protein,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
KeywordsSARS-CoV-2 / SpyTag / VLP / Receptor-binding domain / vaccine / COVID-19 / SpyCatcher / nanocage / icosahedral / nanoparticle / coronavirus / mi3 / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


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 / SDR-like Ig domain / Bacterial Ig domain / KDPG/KHG aldolase / KDPG and KHG aldolase ...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 / SDR-like Ig domain / Bacterial Ig domain / KDPG/KHG aldolase / KDPG and KHG aldolase / 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 speciesHuman immunodeficiency virus 1 / Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDuyvesteyn HME / Stuart DI
Funding support United Kingdom, 1 items
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, 2020-
Header (metadata) releaseJan 13, 2021-
Map releaseJan 13, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.193
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.193
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b3y
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7b3y
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11997.png

Downloads & links

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Map

FileDownload / File: emd_11997.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRBD Spy mi3 cage vlp
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 280 pix.
= 456.4 Å		1.63 Å/pix.
x 280 pix.
= 456.4 Å		1.63 Å/pix.
x 280 pix.
= 456.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.63 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.193 / Movie #1: 0.193
Minimum - Maximum-0.2755475 - 0.8551857
Average (Standard dev.)0.0011880954 (±0.039292116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-140-140-140
Dimensions280280280
Spacing280280280
CellA=B=C: 456.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.631.631.63
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z456.400456.400456.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS-140-140-140
NC/NR/NS280280280
D min/max/mean-0.2760.8550.001

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Supplemental data

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Sample components

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Entire : RBD-Spycatcher-mi3

EntireName: RBD-Spycatcher-mi3
Components
  • Complex: RBD-Spycatcher-mi3
    • Protein or peptide: Fibronectin binding protein,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

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Supramolecule #1: RBD-Spycatcher-mi3

SupramoleculeName: RBD-Spycatcher-mi3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: Fibronectin binding protein,2-dehydro-3-deoxyphosphogluconate ald...

MacromoleculeName: Fibronectin binding protein,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
type: protein_or_peptide / ID: 1
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.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
Molecular weightTheoretical: 36.000715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSVTTLSG LSGEQGPSGD MTTEEDSATH IKFSKRDEDG RELAGATMEL RDSSGKTIST WISDGHVKDF YLYPGKYTFV ETAAPDGYE VATPIEFTVN EDGQVTVDGE ATEGDAHTGG SGGSGGSGGS MKMEELFKKH KIVAVLRANS VEEAKKKALA V FLGGVHLI ...String:
MGSSVTTLSG LSGEQGPSGD MTTEEDSATH IKFSKRDEDG RELAGATMEL RDSSGKTIST WISDGHVKDF YLYPGKYTFV ETAAPDGYE VATPIEFTVN EDGQVTVDGE ATEGDAHTGG SGGSGGSGGS MKMEELFKKH KIVAVLRANS VEEAKKKALA V FLGGVHLI EITFTVPDAD TVIKELSFLK EMGAIIGAGT VTSVEQARKA VESGAEFIVS PHLDEEISQF AKEKGVFYMP GV MTPTELV KAMKLGHTIL KLFPGEVVGP QFVKAMKGPF PNVKFVPTGG VNLDNVCEWF KAGVLAVGVG SALVKGTPVE VAE KAKAFV EKIRGCTEGS GEPEA

UniProtKB: Fibronectin binding protein, 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.9 mg/mL
BufferpH: 7.5 / Details: PBS
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 7393 / Average electron dose: 48.1 e/Å2
Details: SerialEM collection employing beam tilt for multishots per hole using custom script.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 165000 / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio model.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 150785
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

5kp9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 9.4
Output model

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

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