+Open data
-Basic information
Entry | Database: PDB / ID: 7kjp | |||||||||||||||
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Title | Disulfide Stabilized Norovirus GI.1 VLP Shell Region | |||||||||||||||
Components | Capsid protein VP1 | |||||||||||||||
Keywords | VIRUS LIKE PARTICLE / Norovirus / Stabilized / VLP / Shell | |||||||||||||||
Function / homology | Function and homology information T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding Similarity search - Function | |||||||||||||||
Biological species | Norwalk virus | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.86 Å | |||||||||||||||
Authors | Gorman, J. / Kwong, P.D. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: NPJ Vaccines / Year: 2020 Title: Disulfide stabilization of human norovirus GI.1 virus-like particles focuses immune response toward blockade epitopes. Authors: Raffaello Verardi / Lisa C Lindesmith / Yaroslav Tsybovsky / Jason Gorman / Gwo-Yu Chuang / Caitlin E Edwards / Paul D Brewer-Jensen / Michael L Mallory / Li Ou / Arne Schön / Wei Shi / Ena ...Authors: Raffaello Verardi / Lisa C Lindesmith / Yaroslav Tsybovsky / Jason Gorman / Gwo-Yu Chuang / Caitlin E Edwards / Paul D Brewer-Jensen / Michael L Mallory / Li Ou / Arne Schön / Wei Shi / Ena S Tully / George Georgiou / Ralph S Baric / Peter D Kwong / Abstract: Human noroviruses are non-enveloped, single-strand RNA viruses that cause pandemic outbreaks of acute gastroenteritis. A bivalent vaccine containing GI.1 and GII.4 virus-like particles (VLPs) has ...Human noroviruses are non-enveloped, single-strand RNA viruses that cause pandemic outbreaks of acute gastroenteritis. A bivalent vaccine containing GI.1 and GII.4 virus-like particles (VLPs) has been shown to be safe and highly immunogenic, but its efficacy and durability have been limited. Here, we show that norovirus GI.1 VLPs are unstable and contain a substantial fraction of dissociated VLP components. Broadly reactive, non-neutralizing antibodies isolated from vaccinated donors bound to the dissociated components, but not to the intact VLPs. Engineering of interprotomer disulfide bonds within the shell domain prevented disassembly of the VLPs, while preserving antibody accessibility to blockade epitopes. Without adjuvant, mice immunized with stabilized GI.1 VLPs developed faster blockade antibody titers compared to immunization with wild-type GI.1 VLPs. In addition, immunization with stabilized particles focused immune responses toward surface-exposed epitopes and away from occluded epitopes. Overall, disulfide-stabilized norovirus GI.1 VLPs elicited improved responses over the non-disulfide-stabilized version, suggesting their promise as candidate vaccines. | |||||||||||||||
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 | 7kjp.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kjp.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 7kjp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kjp_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7kjp_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7kjp_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 7kjp_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/7kjp ftp://data.pdbj.org/pub/pdb/validation_reports/kj/7kjp | HTTPS FTP |
-Related structure data
Related structure data | 22897MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 56664.961 Da / Num. of mol.: 3 / Fragment: shell region Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norwalk virus (strain GI/Human/United States/Norwalk/1968) Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q83884 |
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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: Norovirus Hu/1968/US / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Norovirus Hu/1968/US |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE |
Natural host | Organism: Homo sapiens |
Buffer solution | pH: 7.4 |
Buffer component | Name: PBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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 FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 70.48 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 777 |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | |||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23476 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1IHM | |||||||||||||||||||||||||||
Refine LS restraints |
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