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Yorodumi- PDB-8c6d: Production of antigenically stable enterovirus A71 virus-like par... -
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-Basic information
Entry | Database: PDB / ID: 8c6d | ||||||||||||||||||
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Title | Production of antigenically stable enterovirus A71 virus-like particles in Pichia pastoris as a vaccine candidate. | ||||||||||||||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / EVA71 / Enterovirus / VLP / rsVLP | ||||||||||||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / host cell cytoplasm / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Enterovirus A71 | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||||||||||||||
Authors | Kingston, N.J. / Snowden, J.S. / Stonehouse, N.J. / Rowlands, D.J. / Hogle, J.M. | ||||||||||||||||||
Funding support | United Kingdom, United States, 5items
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Citation | Journal: bioRxiv / Year: 2023 Title: Production of antigenically stable enterovirus A71 virus-like particles in as a vaccine candidate. Authors: Natalie J Kingston / Joseph S Snowden / Agnieszka Martyna / Mona Shegdar / Keith Grehan / Alison Tedcastle / Elaine Pegg / Helen Fox / Andrew J Macadam / Javier Martin / James M Hogle / ...Authors: Natalie J Kingston / Joseph S Snowden / Agnieszka Martyna / Mona Shegdar / Keith Grehan / Alison Tedcastle / Elaine Pegg / Helen Fox / Andrew J Macadam / Javier Martin / James M Hogle / David J Rowlands / Nicola J Stonehouse / Abstract: Enterovirus A71 (EVA71) causes widespread disease in young children with occasional fatal consequences. In common with other picornaviruses, both empty capsids (ECs) and infectious virions are ...Enterovirus A71 (EVA71) causes widespread disease in young children with occasional fatal consequences. In common with other picornaviruses, both empty capsids (ECs) and infectious virions are produced during the viral lifecycle. While initially antigenically indistinguishable from virions, ECs readily convert to an expanded conformation at moderate temperatures. In the closely related poliovirus, these conformational changes result in loss of antigenic sites required to elicit protective immune responses. Whether this is true for EVA71 remains to be determined and is the subject of this investigation. We previously reported the selection of a thermally resistant EVA71 genogroup B2 population using successive rounds of heating and passage. The mutations found in the structural protein-coding region of the selected population conferred increased thermal stability to both virions and naturally produced ECs. Here, we introduced these mutations into a recombinant expression system to produce stabilised virus-like particles (VLPs) in . The stabilised VLPs retain the native virion-like antigenic conformation as determined by reactivity with a specific antibody. Structural studies suggest multiple potential mechanisms of antigenic stabilisation, however, unlike poliovirus, both native and expanded EVA71 particles elicited antibodies able to directly neutralise virus . Therefore, the anti-EVA71 neutralising antibodies are elicited by sites which are not canonically associated with the native conformation, but whether antigenic sites specific to the native conformation provide additional protective responses remains unclear. VLPs are likely to provide cheaper and safer alternatives for vaccine production and these data show that VLP vaccines are comparable with inactivated virus vaccines at inducing neutralising antibodies. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c6d.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c6d.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 8c6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/8c6d ftp://data.pdbj.org/pub/pdb/validation_reports/c6/8c6d | HTTPS FTP |
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-Related structure data
Related structure data | 16450MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 32705.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterovirus A71 / Production host: Komagataella pastoris (fungus) References: UniProt: A0A2L1GIK5, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
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#2: Protein | Mass: 35253.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterovirus A71 / Production host: Komagataella pastoris (fungus) / References: UniProt: D4QGA2 |
#3: Protein | Mass: 26558.369 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterovirus A71 / Production host: Komagataella pastoris (fungus) / References: UniProt: D4QGA4 |
#4: Chemical | ChemComp-SQS / ( |
Has ligand of interest | Y |
-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: Enterovirus A71Enterovirus 71 / Type: VIRUS / Details: rsVLP expressed in Pichia pastoris / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Enterovirus A71 |
Source (recombinant) | Organism: Komagataella pastoris (fungus) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE |
Natural host | Organism: Homo sapiens |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2900 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 31.08 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement |
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EM software | Name: RELION / Category: 3D reconstruction |
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: I (icosahedral) |
3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11789 / Symmetry type: POINT |