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Yorodumi- EMDB-10316: Hepatitis B virus core protein virus-like particle displaying the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10316 | |||||||||
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Title | Hepatitis B virus core protein virus-like particle displaying the antigen: extra cellular adhesion domain NadA from Neisseria meningitidis. | |||||||||
Map data | Hepatitis B virus core protein with the extracellular domain of NadA inserted at the tip of the spikes of the VLP/capsid spikes. | |||||||||
Sample |
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Function / homology | Function and homology information microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / cell outer membrane / viral penetration into host nucleus / host cell / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / viral envelope / structural molecule activity ...microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / cell outer membrane / viral penetration into host nucleus / host cell / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / viral envelope / structural molecule activity / cell surface / DNA binding / RNA binding Similarity search - Function | |||||||||
Biological species | Neisseria meningitidis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Collins RF / Roseman AM / Derrick JP | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Vaccine / Year: 2020 Title: An assessment of the use of Hepatitis B Virus core protein virus-like particles to display heterologous antigens from Neisseria meningitidis. Authors: Sebastian Aston-Deaville / Emil Carlsson / Muhammad Saleem / Angela Thistlethwaite / Hannah Chan / Sunil Maharjan / Alessandra Facchetti / Ian M Feavers / C Alistair Siebert / Richard F ...Authors: Sebastian Aston-Deaville / Emil Carlsson / Muhammad Saleem / Angela Thistlethwaite / Hannah Chan / Sunil Maharjan / Alessandra Facchetti / Ian M Feavers / C Alistair Siebert / Richard F Collins / Alan Roseman / Jeremy P Derrick / Abstract: Neisseria meningitidis is the causative agent of meningococcal meningitis and sepsis and remains a significant public health problem in many countries. Efforts to develop a comprehensive vaccine ...Neisseria meningitidis is the causative agent of meningococcal meningitis and sepsis and remains a significant public health problem in many countries. Efforts to develop a comprehensive vaccine against serogroup B meningococci have focused on the use of surface-exposed outer membrane proteins. Here we report the use of virus-like particles derived from the core protein of Hepatitis B Virus, HBc, to incorporate antigen domains derived from Factor H binding protein (FHbp) and the adhesin NadA. The extracellular domain of NadA was inserted into the major immunodominant region of HBc, and the C-terminal domain of FHbp at the C-terminus (CFHbp), creating a single polypeptide chain 3.7-fold larger than native HBc. Remarkably, cryoelectron microscopy revealed that the construct formed assemblies that were able to incorporate both antigens with minimal structural changes to native HBc. Electron density was weak for NadA and absent for CFHbp, partly attributable to domain flexibility. Following immunization of mice, three HBc fusions (CFHbp or NadA alone, NadA + CFHbp) were able to induce production of IgG1, IgG2a and IgG2b antibodies reactive against their respective antigens at dilutions in excess of 1:18,000. However, only HBc fusions containing NadA elicited the production of antibodies with serum bactericidal activity. It is hypothesized that this improved immune response is attributable to the adoption of a more native-like folding of crucial conformational epitopes of NadA within the chimeric VLP. This work demonstrates that HBc can incorporate insertions of large antigen domains but that maintenance of their three-dimensional structure is likely to be critical in obtaining a protective response. | |||||||||
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_10316.map.gz | 483.5 MB | EMDB map data format | |
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Header (meta data) | emd-10316-v30.xml emd-10316.xml | 23.1 KB 23.1 KB | Display Display | EMDB header |
Images | emd_10316.png | 199 KB | ||
Others | emd_10316_additional_1.map.gz emd_10316_additional_2.map.gz emd_10316_half_map_1.map.gz emd_10316_half_map_2.map.gz | 253.6 MB 253.6 MB 475.3 MB 475.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10316 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10316 | HTTPS FTP |
-Validation report
Summary document | emd_10316_validation.pdf.gz | 371.8 KB | Display | EMDB validaton report |
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Full document | emd_10316_full_validation.pdf.gz | 370.9 KB | Display | |
Data in XML | emd_10316_validation.xml.gz | 16.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10316 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10316 | HTTPS FTP |
-Related structure data
Related structure data | 6tikMC 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_10316.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Hepatitis B virus core protein with the extracellular domain of NadA inserted at the tip of the spikes of the VLP/capsid spikes. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_10316_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Mask for FSC calculation
File | emd_10316_additional_2.map | ||||||||||||
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Annotation | Mask for FSC calculation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A.
File | emd_10316_half_map_1.map | ||||||||||||
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Annotation | Half map A. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B.
File | emd_10316_half_map_2.map | ||||||||||||
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Annotation | Half map B. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : VLP fusion sequence expressed in E.coli.
Entire | Name: VLP fusion sequence expressed in E.coli. |
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Components |
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-Supramolecule #1: VLP fusion sequence expressed in E.coli.
Supramolecule | Name: VLP fusion sequence expressed in E.coli. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: HBcS-NadA-CFHbp Fusion protein with linker regions. HBc - Ordered core of VLP: from HBV core protein (NCBI taxonomy ID 10407). NadA - Partially ordered surface displayed domain: ...Details: HBcS-NadA-CFHbp Fusion protein with linker regions. HBc - Ordered core of VLP: from HBV core protein (NCBI taxonomy ID 10407). NadA - Partially ordered surface displayed domain: extracellular domain of NadA from Neisseria meningitidis (NCBI taxonomy ID 487). CFHbp - Unresolved/disordered component : C-terminal domain of factor H binding protein from Neisseria meningitidis (NCBI taxonomy ID 487). |
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Source (natural) | Organism: Neisseria meningitidis (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: pET-17b |
Molecular weight | Theoretical: 14.9 MDa |
-Macromolecule #1: HBcS-NadA-CFHbp
Macromolecule | Name: HBcS-NadA-CFHbp / type: protein_or_peptide / ID: 1 / Details: expressed fusion chimera protein / Enantiomer: LEVO |
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Sequence | String: MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAI LCWGELMTLA TWVGNNLEDG GGGSGGGGSA TSDDDVKKAA TVAIVAAYNN GQEINGFKAG ETIYDIGED GTITQKDATA ADVEADDFKG LGLKKVVTNL TKTVNENKQN ...String: MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAI LCWGELMTLA TWVGNNLEDG GGGSGGGGSA TSDDDVKKAA TVAIVAAYNN GQEINGFKAG ETIYDIGED GTITQKDATA ADVEADDFKG LGLKKVVTNL TKTVNENKQN VDAKVKAAES E IEKLTTKL ADTDAALADT DAALDETTNA LNKLGENITT FAEETKTNIV KIDEKLEAVA DT VDKHAEA FNDIADSLDE TNTKADEAVK TANEAKQTAE ETKQNVDAKV KAAETAAGKA EAA AGTANT AADKAEAVAA KVTDIKADIA TNKADIAKNS ARIDSLDKNV ANLRKETRQG LAEQ AALSG LFQPYNVGEF GGGGSGGGGS RDLVVNYVNT NMGLKIRQLL WFHISCLTFG RETVL EYLV SFGVWIRTPP AYRPPNAPIL STLPETTVVG SGGGTHTSFD KLPEGGRATY RGTAFG SDD AGGKLTYTID FAAKQGNGKI EHLKSPELNV DLAAADIKPD GKRHAVISGS VLYNQAE KG SYSLGIFGGK AQEVAGSAEV KTVNGIRHIG LAAKQKLGGG WSHPQFEK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 / Details: PBS |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: 3 ul applied for 30s at room temperature, then 4-5 s blot.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 3-36 / Number grids imaged: 1 / Number real images: 2367 / Average exposure time: 4.0 sec. / Average electron dose: 79.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.84 µm / Calibrated defocus min: 0.424 µm / Calibrated magnification: 100719 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0025 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 104167 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |