+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22897 | |||||||||||||||
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Title | Disulfide Stabilized Norovirus GI.1 VLP Shell Region | |||||||||||||||
Map data | Sharpened map | |||||||||||||||
Sample |
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Function / homology | Function and homology information T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding Similarity search - Function | |||||||||||||||
Biological species | Norwalk virus (strain GI/Human/United States/Norwalk/1968) / Norovirus Hu/1968/US | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.86 Å | |||||||||||||||
Authors | Gorman J / Kwong PD | |||||||||||||||
Funding support | United States, 4 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22897.map.gz | 772.8 MB | EMDB map data format | |
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Header (meta data) | emd-22897-v30.xml emd-22897.xml | 20 KB 20 KB | Display Display | EMDB header |
Images | emd_22897.png | 313.3 KB | ||
Masks | emd_22897_msk_1.map | 824 MB | Mask map | |
Others | emd_22897_additional_1.map.gz emd_22897_half_map_1.map.gz emd_22897_half_map_2.map.gz | 170.5 MB 755.4 MB 756.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22897 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22897 | HTTPS FTP |
-Validation report
Summary document | emd_22897_validation.pdf.gz | 803.3 KB | Display | EMDB validaton report |
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Full document | emd_22897_full_validation.pdf.gz | 802.8 KB | Display | |
Data in XML | emd_22897_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | emd_22897_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22897 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22897 | HTTPS FTP |
-Related structure data
Related structure data | 7kjpMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22897.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07325 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_22897_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_22897_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_22897_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_22897_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Norovirus Hu/1968/US
Entire | Name: Norovirus Hu/1968/US |
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Components |
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-Supramolecule #1: Norovirus Hu/1968/US
Supramolecule | Name: Norovirus Hu/1968/US / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 524364 / Sci species name: Norovirus Hu/1968/US / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) |
Host system | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Norwalk virus (strain GI/Human/United States/Norwalk/1968) Strain: GI/Human/United States/Norwalk/1968 |
Molecular weight | Theoretical: 56.664961 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MMMASKDATS SVDGASGAGQ LVPEVNASDP LAMDPVAGSS TAVATAGQVN PIDPWIINNF VQAPQGEFTI SPNNTPGDVL FDLSLGPHL NPFLLHLSQM YNGWVGNMRV RIMLAGCAFT AGKIIVSCIP PGFGSHNLTI AQATLFPHVI ADVRTLDPIE V PLEDVRNV ...String: MMMASKDATS SVDGASGAGQ LVPEVNASDP LAMDPVAGSS TAVATAGQVN PIDPWIINNF VQAPQGEFTI SPNNTPGDVL FDLSLGPHL NPFLLHLSQM YNGWVGNMRV RIMLAGCAFT AGKIIVSCIP PGFGSHNLTI AQATLFPHVI ADVRTLDPIE V PLEDVRNV LFHNNDRNQQ TMRLVCMLYT PLRTCGGTGD SFVVAGRVMT CPSPDFNFLF LVPPTVEQKT RPFTLPNLPL SS LSNSRAP LPISSMGISP DNVQSVQFQN GRCTLDGRLV GTTPVSLSHV AKIRGTSNGT VINLTELDGT PFHPFEGPAP IGF PDLGGC DWHINMTQFG HSSQTQYDVD TTPDTFVPHL GSIQANGIGS GNYVGVLSWI SPPSHPSGSQ VDLWKIPNYG SSIT EATHL APSVYPPGFG EVLVFFMSKM PGPGAYNLPC LLPQEYISHL ASEQAPTVGE AALLHYVDPD TGRNLGEFKA YPDGF LTCV PNGASSGPQQ LPINGVFVFV SWVSRFYQLK PVGTASSARG RLGLRR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Component - Name: PBS |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 777 / Average electron dose: 70.48 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |