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Yorodumi- PDB-6hcr: Synthetic Self-assembling ADDomer Platform for Highly Efficient V... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hcr | ||||||
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Title | Synthetic Self-assembling ADDomer Platform for Highly Efficient Vaccination by Genetically-encoded Multi-epitope Display | ||||||
Components | Penton protein | ||||||
Keywords | VIRUS LIKE PARTICLE / engineered / virus / like / particle / ADDomer / Ad3 / penton / base / adenovirus / synthetic / vaccine / biobrick / human / homosapien / dodecahedron / icosohedral / epitode / display / scaffold | ||||||
Function / homology | Adenovirus 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 species | Human adenovirus B serotype 3 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Bufton, J.C. / Berger, I. / Schaffitzel, C. / Garzoni, F. / Rabi, F.A. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6hcr.cif.gz | 4.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6hcr.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6hcr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hcr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6hcr_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6hcr_validation.xml.gz | 580.2 KB | Display | |
Data in CIF | 6hcr_validation.cif.gz | 893.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/6hcr ftp://data.pdbj.org/pub/pdb/validation_reports/hc/6hcr | HTTPS FTP |
-Related structure data
Related structure data | 0198MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 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 |
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Molecular weight | Value: 3.811834 MDa / Experimental value: NO |
Source (natural) | Organism: Human adenovirus B3 |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Image recording | Average 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 scans | Movie frames/image: 32 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1758 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: 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 building | PDB-ID: 4AR2 Pdb chain-ID: A / Accession code: 4AR2 / Pdb chain residue range: 61-542 / Source name: PDB / Type: experimental model |