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Yorodumi- EMDB-28807: Cryo-EM structure of Lumazine synthase nanoparticle linked to VP8... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28807 | |||||||||
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Title | Cryo-EM structure of Lumazine synthase nanoparticle linked to VP8* antigen | |||||||||
Map data | Cryo-EM structure of Lumazine synthase nanoparticle linked to VP8* antigen | |||||||||
Sample |
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Keywords | Rotavirus / VP8* / lumazine synthase / nanoparticle / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information 6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / cytosol Similarity search - Function | |||||||||
Biological species | Aquifex aeolicus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Mangala Prasad V / Lee KK | |||||||||
Funding support | United States, 1 items
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Citation | Journal: NPJ Vaccines / Year: 2023 Title: mRNA-based VP8* nanoparticle vaccines against rotavirus are highly immunogenic in rodents. Authors: Sandro Roier / Vidya Mangala Prasad / Monica M McNeal / Kelly K Lee / Benjamin Petsch / Susanne Rauch / Abstract: Despite the availability of live-attenuated oral vaccines, rotavirus remains a major cause of severe childhood diarrhea worldwide. Due to the growing demand for parenteral rotavirus vaccines, we ...Despite the availability of live-attenuated oral vaccines, rotavirus remains a major cause of severe childhood diarrhea worldwide. Due to the growing demand for parenteral rotavirus vaccines, we developed mRNA-based vaccine candidates targeting the viral spike protein VP8*. Our monomeric P2 (universal T cell epitope)-VP8* mRNA design is equivalent to a protein vaccine currently in clinical development, while LS (lumazine synthase)-P2-VP8* was designed to form nanoparticles. Cyro-electron microscopy and western blotting-based data presented here suggest that proteins derived from LS-P2-VP8* mRNA are secreted in vitro and self-assemble into 60-mer nanoparticles displaying VP8*. mRNA encoded VP8* was immunogenic in rodents and introduced both humoral and cellular responses. LS-P2-VP8* induced superior humoral responses to P2-VP8* in guinea pigs, both as monovalent and trivalent vaccines, with encouraging responses detected against the most prevalent P genotypes. Overall, our data provide evidence that trivalent LS-P2-VP8* represents a promising mRNA-based next-generation rotavirus vaccine candidate. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28807.map.gz | 34.3 MB | EMDB map data format | |
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Header (meta data) | emd-28807-v30.xml emd-28807.xml | 16 KB 16 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28807_fsc.xml | 10.2 KB | Display | FSC data file |
Images | emd_28807.png | 232.1 KB | ||
Filedesc metadata | emd-28807.cif.gz | 5.6 KB | ||
Others | emd_28807_half_map_1.map.gz emd_28807_half_map_2.map.gz | 71.3 MB 71.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28807 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28807 | HTTPS FTP |
-Validation report
Summary document | emd_28807_validation.pdf.gz | 840.7 KB | Display | EMDB validaton report |
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Full document | emd_28807_full_validation.pdf.gz | 840.3 KB | Display | |
Data in XML | emd_28807_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | emd_28807_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28807 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28807 | HTTPS FTP |
-Related structure data
Related structure data | 8f25MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28807.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of Lumazine synthase nanoparticle linked to VP8* antigen | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half-map2
File | emd_28807_half_map_1.map | ||||||||||||
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Annotation | Half-map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map
File | emd_28807_half_map_2.map | ||||||||||||
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Annotation | Half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Lumazine synthase nanoparticle linked to rotatvirus VP8* protein
Entire | Name: Lumazine synthase nanoparticle linked to rotatvirus VP8* protein |
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Components |
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-Supramolecule #1: Lumazine synthase nanoparticle linked to rotatvirus VP8* protein
Supramolecule | Name: Lumazine synthase nanoparticle linked to rotatvirus VP8* protein type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Aquifex aeolicus (bacteria) |
Molecular weight | Theoretical: 2.7 MDa |
-Macromolecule #1: 6,7-dimethyl-8-ribityllumazine synthase
Macromolecule | Name: 6,7-dimethyl-8-ribityllumazine synthase / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase |
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Source (natural) | Organism: Aquifex aeolicus (bacteria) / Strain: VF5 |
Molecular weight | Theoretical: 16.728186 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEIYEGKLTA EGLRFGIVAS RFNHALVDRL VEGAIDCIVR HGGREEDITL VRVPGSWEIP VAAGELARKE DIDAVIAIGV LIRGATPHF DYIASEVSKG LANLSLELRK PITFGVITAD TLEQAIERAG TKHGNKGWEA ALSAIEMANL FKSLR UniProtKB: 6,7-dimethyl-8-ribityllumazine synthase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.4 / Details: Phosphate Buffer Saline |
Grid | Model: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | monodisperse sample in PBS |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 10.0 sec. / Average electron dose: 284.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | Rigid body fitting followed by default Real space refinement in phenix with only rigid body fitting and occupancy refinement |
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Refinement | Protocol: RIGID BODY FIT |
Output model | PDB-8f25: |