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- PDB-6hcr: Synthetic Self-assembling ADDomer Platform for Highly Efficient V... -

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Basic information

Entry
Database: PDB / ID: 6hcr
TitleSynthetic Self-assembling ADDomer Platform for Highly Efficient Vaccination by Genetically-encoded Multi-epitope Display
ComponentsPenton protein
KeywordsVIRUS LIKE PARTICLE / engineered / virus / like / particle / ADDomer / Ad3 / penton / base / adenovirus / synthetic / vaccine / biobrick / human / homosapien / dodecahedron / icosohedral / epitode / display / scaffold
Function / homologyAdenovirus penton base protein / Adenovirus penton base protein / T=25 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding / Penton protein
Function and homology information
Biological speciesHuman adenovirus B serotype 3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBufton, J.C. / Berger, I. / Schaffitzel, C. / Garzoni, F. / Rabi, F.A.
CitationJournal: Sci Adv / Year: 2019
Title: Synthetic self-assembling ADDomer platform for highly efficient vaccination by genetically encoded multiepitope display.
Authors: Charles Vragniau / Joshua C Bufton / Frédéric Garzoni / Emilie Stermann / Fruzsina Rabi / Céline Terrat / Mélanie Guidetti / Véronique Josserand / Matt Williams / Christopher J Woods / ...Authors: Charles Vragniau / Joshua C Bufton / Frédéric Garzoni / Emilie Stermann / Fruzsina Rabi / Céline Terrat / Mélanie Guidetti / Véronique Josserand / Matt Williams / Christopher J Woods / Gerardo Viedma / Phil Bates / Bernard Verrier / Laurence Chaperot / Christiane Schaffitzel / Imre Berger / Pascal Fender /
Abstract: Self-assembling virus-like particles represent highly attractive tools for developing next-generation vaccines and protein therapeutics. We created ADDomer, an adenovirus-derived multimeric protein- ...Self-assembling virus-like particles represent highly attractive tools for developing next-generation vaccines and protein therapeutics. We created ADDomer, an adenovirus-derived multimeric protein-based self-assembling nanoparticle scaffold engineered to facilitate plug-and-play display of multiple immunogenic epitopes from pathogens. We used cryo-electron microscopy at near-atomic resolution and implemented novel, cost-effective, high-performance cloud computing to reveal architectural features in unprecedented detail. We analyzed ADDomer interaction with components of the immune system and developed a promising first-in-kind ADDomer-based vaccine candidate to combat emerging Chikungunya infectious disease, exemplifying the potential of our approach.
History
DepositionAug 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
z: 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
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
u: Penton protein
v: Penton protein
w: Penton protein
x: Penton protein
y: Penton protein
1: Penton protein
2: Penton protein
3: Penton protein
4: Penton protein
5: Penton protein
6: Penton protein
7: Penton protein
8: Penton protein
9: Penton protein


Theoretical massNumber of molelcules
Total (without water)3,815,89860
Polymers3,815,89860
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Purified by Sucrose Gradient and Gel filtration followed by Negative stain/Cryo-EM analysis., equilibrium centrifugation, Observed via Sucrose Gradient, Gel ...Evidence: equilibrium centrifugation, Purified by Sucrose Gradient and Gel filtration followed by Negative stain/Cryo-EM analysis., equilibrium centrifugation, Observed via Sucrose Gradient, Gel filtration and in negative stain/cryo electron micrographs.
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

#1: Protein ...
Penton protein / CP-P / Penton base protein / Protein III


Mass: 63598.293 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus B serotype 3 / Gene: L2
Cell line (production host): High Five Cells (BTI-TN-5B1-4)
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: An engineered viral like particle derived from penton base protein of Human adenovirus B3 (Ad3).
Type: COMPLEX
Details: Recombinantly expressed and purified ADDomer complex (penton base dodecahedron).
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 3.811834 MDa / Experimental value: NO
Source (natural)Organism: Human adenovirus B3
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen 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: 3200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 1.3125 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1060
Image scansMovie frames/image: 32

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Processing

EM software
IDNameVersionCategoryDetails
1RELION2.1particle selection
2RELION2.2image acquisition
4CTFFIND4.1CTF correction
7Coot0.8.9model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.13model refinementReal space refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1758 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
Details: The model was adjusted to fit into the map manually using COOT before further iterative positional and B-factor refinement in real space using Phenix Real-Space refinement software. Final ...Details: The model was adjusted to fit into the map manually using COOT before further iterative positional and B-factor refinement in real space using Phenix Real-Space refinement software. Final adjustments were carried out in COOT.
Atomic model buildingPDB-ID: 4AR2

4ar2


Pdb chain-ID: A / Accession code: 4AR2 / Pdb chain residue range: 61-542 / Source name: PDB / Type: experimental model

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