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- PDB-8c9n: MiniCoV-ADDomer, a SARS-CoV-2 epitope presenting viral like particle -

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Basic information

Entry
Database: PDB / ID: 8c9n
TitleMiniCoV-ADDomer, a SARS-CoV-2 epitope presenting viral like particle
ComponentsPenton protein
KeywordsVIRUS LIKE PARTICLE / ADDomer / VLP / Viral / like / Particle / AD3 / Penton / base / vaccine / COVID-19 / COVID / MINI-COVID / Dodecahedron / pb / protein / adenovirus / human
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.36 Å
AuthorsBufton, J.C. / Capin, J. / Boruku, U. / Garzoni, F. / Schaffitzel, C. / Berger, I.
Funding support United Kingdom, 8items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Penton protein
A: Penton protein
B: Penton protein
C: Penton protein
D: Penton protein
E: Penton protein
F: Penton protein
G: Penton protein
H: Penton protein
I: Penton protein
J: Penton protein
K: Penton protein
L: Penton protein
M: Penton protein
N: Penton protein
O: Penton protein
P: Penton protein
Q: Penton protein
R: Penton protein
S: Penton protein
T: Penton protein
V: Penton protein
W: Penton protein
X: Penton protein
Y: Penton protein
Z: Penton protein
AA: Penton protein
BA: Penton protein
CA: Penton protein
DA: Penton protein
EA: Penton protein
FA: Penton protein
GA: Penton protein
HA: Penton protein
IA: Penton protein
JA: Penton protein
KA: Penton protein
LA: Penton protein
MA: Penton protein
NA: Penton protein
OA: Penton protein
PA: Penton protein
QA: Penton protein
RA: Penton protein
SA: Penton protein
TA: Penton protein
UA: Penton protein
VA: Penton protein
WA: Penton protein
XA: Penton protein
YA: Penton protein
ZA: Penton protein
AB: Penton protein
BB: Penton protein
CB: Penton protein
DB: Penton protein
EB: Penton protein
FB: Penton protein
GB: Penton protein
HB: Penton protein


Theoretical massNumber of molelcules
Total (without water)3,997,11360
Polymers3,997,11360
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area360850 Å2
ΔGint-1517 kcal/mol
Surface area1043630 Å2

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Components

#1: Protein ...
Penton protein


Mass: 66618.547 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus B3 / Gene: L2 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q2Y0H9

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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: ADDomer Mini-COVID viral like particle vaccine derived from Human Ad3 penton base protein.
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 3.9930516 MDa / Experimental value: NO
Source (natural)Organism: Human adenovirus B3
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Image recordingElectron dose: 1.1 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4Gctf1.18b2CTF correction
7Coot0.8.9.2model fitting
9PHENIX1.12-2829-000model refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 96546
3D reconstructionResolution: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32227 / Symmetry type: POINT

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