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- EMDB-16512: MiniCoV-ADDomer, a SARS-CoV-2 epitope presenting viral like particle -

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Basic information

Entry
Database: EMDB / ID: EMD-16512
TitleMiniCoV-ADDomer, a SARS-CoV-2 epitope presenting viral like particle
Map data
Sample
  • Complex: ADDomer Mini-COVID viral like particle vaccine derived from Human Ad3 penton base protein.
    • Protein or peptide: Penton protein
KeywordsADDomer / VLP / Viral / like / Particle / AD3 / Penton / base / vaccine / COVID-19 / COVID / MINI-COVID / Dodecahedron / pb / protein / adenovirus / human / VIRUS LIKE PARTICLE
Function / homologyAdenovirus penton base protein / Adenovirus penton base protein / T=25 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding / Penton protein
Function and homology information
Biological speciesHuman adenovirus B3
Methodsingle particle reconstruction / cryo EM / Resolution: 2.36 Å
AuthorsBufton JC / Capin J / Boruku U / Garzoni F / Schaffitzel C / Berger I
Funding support United Kingdom, 8 items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/R511663/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Wellcome Trust202904/Z/16/Z United Kingdom
Wellcome Trust206181/Z/17/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R000484/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/R013764/1 United Kingdom
Wellcome Trust210701/Z/18/Z United Kingdom
Wellcome Trust106115/Z/14/Z United Kingdom
CitationJournal: Antib Ther / Year: 2023
Title: generated antibodies guide thermostable ADDomer nanoparticle design for nasal vaccination and passive immunization against SARS-CoV-2.
Authors: Dora Buzas / Adrian H Bunzel / Oskar Staufer / Emily J Milodowski / Grace L Edmunds / Joshua C Bufton / Beatriz V Vidana Mateo / Sathish K N Yadav / Kapil Gupta / Charlotte Fletcher / Maia K ...Authors: Dora Buzas / Adrian H Bunzel / Oskar Staufer / Emily J Milodowski / Grace L Edmunds / Joshua C Bufton / Beatriz V Vidana Mateo / Sathish K N Yadav / Kapil Gupta / Charlotte Fletcher / Maia K Williamson / Alexandra Harrison / Ufuk Borucu / Julien Capin / Ore Francis / Georgia Balchin / Sophie Hall / Mirella V Vega / Fabien Durbesson / Srikanth Lingappa / Renaud Vincentelli / Joe Roe / Linda Wooldridge / Rachel Burt / Ross J L Anderson / Adrian J Mulholland / Bristol Uncover Group / Jonathan Hare / Mick Bailey / Andrew D Davidson / Adam Finn / David Morgan / Jamie Mann / Joachim Spatz / Frederic Garzoni / Christiane Schaffitzel / Imre Berger /
Abstract: BACKGROUND: Due to COVID-19, pandemic preparedness emerges as a key imperative, necessitating new approaches to accelerate development of reagents against infectious pathogens.
METHODS: Here, we developed an integrated approach combining synthetic, computational and structural methods with antibody selection and immunization to design, produce and validate nature-inspired ...METHODS: Here, we developed an integrated approach combining synthetic, computational and structural methods with antibody selection and immunization to design, produce and validate nature-inspired nanoparticle-based reagents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
RESULTS: Our approach resulted in two innovations: (i) a thermostable nasal vaccine called ADDoCoV, displaying multiple copies of a SARS-CoV-2 receptor binding motif derived epitope and (ii) a ...RESULTS: Our approach resulted in two innovations: (i) a thermostable nasal vaccine called ADDoCoV, displaying multiple copies of a SARS-CoV-2 receptor binding motif derived epitope and (ii) a multivalent nanoparticle superbinder, called Gigabody, against SARS-CoV-2 including immune-evasive variants of concern (VOCs). generated neutralizing nanobodies and electron cryo-microscopy established authenticity and accessibility of epitopes displayed by ADDoCoV. Gigabody comprising multimerized nanobodies prevented SARS-CoV-2 virion attachment with picomolar EC. Vaccinating mice resulted in antibodies cross-reacting with VOCs including Delta and Omicron.
CONCLUSION: Our study elucidates Adenovirus-derived dodecamer (ADDomer)-based nanoparticles for use in active and passive immunization and provides a blueprint for crafting reagents to combat ...CONCLUSION: Our study elucidates Adenovirus-derived dodecamer (ADDomer)-based nanoparticles for use in active and passive immunization and provides a blueprint for crafting reagents to combat respiratory viral infections.
History
DepositionJan 23, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16512.png

Downloads & links

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Map

FileDownload / File: emd_16512.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 340 pix.
= 357. Å		1.05 Å/pix.
x 340 pix.
= 357. Å		1.05 Å/pix.
x 340 pix.
= 357. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.015942328 - 0.07183091
Average (Standard dev.)0.0007413957 (±0.005724614)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 356.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16512_half_map_1.map
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Half map: #2

Fileemd_16512_half_map_2.map
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Sample components

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Entire : ADDomer Mini-COVID viral like particle vaccine derived from Human...

EntireName: ADDomer Mini-COVID viral like particle vaccine derived from Human Ad3 penton base protein.
Components
  • Complex: ADDomer Mini-COVID viral like particle vaccine derived from Human Ad3 penton base protein.
    • Protein or peptide: Penton protein

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Supramolecule #1: ADDomer Mini-COVID viral like particle vaccine derived from Human...

SupramoleculeName: ADDomer Mini-COVID viral like particle vaccine derived from Human Ad3 penton base protein.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human adenovirus B3
Molecular weightTheoretical: 3.9930516 MDa

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Macromolecule #1: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Human adenovirus B3
Molecular weightTheoretical: 66.618547 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MRRRAVLGGA VVYPEGPPPS YESVMQQQAA MIQPPLEAPF VPPRYLAPTE GRNSIRYSEL SPLYDTTKLY LVDNKSADIA SLNYQNDHS NFLTTVVQNN DFTPTEASTQ TINFDERSRW GGQLKTIMHT NMPNVNEYMF SNKFKARVMV SRKAPEGEFY Q AGSTPCNG ...String:
MRRRAVLGGA VVYPEGPPPS YESVMQQQAA MIQPPLEAPF VPPRYLAPTE GRNSIRYSEL SPLYDTTKLY LVDNKSADIA SLNYQNDHS NFLTTVVQNN DFTPTEASTQ TINFDERSRW GGQLKTIMHT NMPNVNEYMF SNKFKARVMV SRKAPEGEFY Q AGSTPCNG VEGFNCYFPL QSYGFQPTNG VGYGPVNDTY DHKEDILKYE WFEFILPEGN FSATMTIDLM NNAIIDNYLE IG RQNGVLE SDIGVKFDTR NFRLGWDPET KLIMPGVYTY EAFHPDIVLL PGCGVDFTES RLSNLLGIRK RHPFQEGFKI MYE DLEGGN IPALLDVTAY EESKKDTTTA RETTTLAVAE ETSEDVDDDI TRGDTYITEL EKQKREAAAA EVSRKKELKI QPLE KDSKS RSYNVLEDKI NTAYRSWYLS YNYGNPEKGI RSWTLLTTSD VTCGAEQVYW SLPDMMQDPV TFRSTRQVNN YPVVG AELM PVFSKSFYNE QAVYSQQLRQ ATSLTHVFNR FPENQILIRP PAPTITTVSE NVPALTDHGT LPLRSSIRGV QRVTVT DAR RRTCPYVYKA LGIVAPRVLS SRTF

UniProtKB: Penton protein

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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

Concentration0.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.1 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 96546
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6hcr

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 32227
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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