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- EMDB-6926: CryoEM structure of mature dengue virus-like particle at 13 Angst... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6926 | |||||||||
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Title | CryoEM structure of mature dengue virus-like particle at 13 Angstroms resolution | |||||||||
![]() | The single particle cryo-EM reconstruction of highly matured virus-like particles derived from DENV serotype 2 (mD2VLP). The images analyses were performed using EMAN2. | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.0 Å | |||||||||
![]() | Wu SR / Chao DY | |||||||||
![]() | ![]() Title: Epitope resurfacing on dengue virus-like particle vaccine preparation to induce broad neutralizing antibody. Authors: Wen-Fan Shen / Jedhan Ucat Galula / Jyung-Hurng Liu / Mei-Ying Liao / Cheng-Hao Huang / Yu-Chun Wang / Han-Chung Wu / Jian-Jong Liang / Yi-Ling Lin / Matthew T Whitney / Gwong-Jen J Chang / ...Authors: Wen-Fan Shen / Jedhan Ucat Galula / Jyung-Hurng Liu / Mei-Ying Liao / Cheng-Hao Huang / Yu-Chun Wang / Han-Chung Wu / Jian-Jong Liang / Yi-Ling Lin / Matthew T Whitney / Gwong-Jen J Chang / Sheng-Ren Chen / Shang-Rung Wu / Day-Yu Chao / ![]() ![]() Abstract: Dengue fever is caused by four different serotypes of dengue virus (DENV) which is the leading cause of worldwide arboviral diseases in humans. Virus-like particles (VLPs) containing flavivirus prM/E ...Dengue fever is caused by four different serotypes of dengue virus (DENV) which is the leading cause of worldwide arboviral diseases in humans. Virus-like particles (VLPs) containing flavivirus prM/E proteins have been demonstrated to be a potential vaccine candidate; however, the structure of dengue VLP is poorly understood. Herein VLP derived from DENV serotype-2 were engineered becoming highly matured (mD2VLP) and showed variable size distribution with diameter of ~31 nm forming the major population under cryo-electron microscopy examination. Furthermore, mD2VLP particles of 31 nm diameter possess a T = 1 icosahedral symmetry with a groove located within the E-protein dimers near the 2-fold vertices that exposed highly overlapping, cryptic neutralizing epitopes. Mice vaccinated with mD2VLP generated higher cross-reactive (CR) neutralization antibodies (NtAbs) and were fully protected against all 4 serotypes of DENV. Our results highlight the potential of 'epitope-resurfaced' mature-form D2VLPs in inducing quaternary structure-recognizing broad CR NtAbs to guide future dengue vaccine design. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.3 KB 12.3 KB | Display Display | ![]() |
Images | ![]() | 125.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.1 KB | Display | ![]() |
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Full document | ![]() | 77.2 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The single particle cryo-EM reconstruction of highly matured virus-like particles derived from DENV serotype 2 (mD2VLP). The images analyses were performed using EMAN2. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : dengue virus serotype 2
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: dengue virus serotype 2
Supramolecule | Name: dengue virus serotype 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: The particles were produced from recombinant plasmid pVD2, expressing the prM, 80% and 20% COOH terminus of the envelope proteins of DENV-2 (Asian 1 genotype, strain 16681) and Japanese ...Details: The particles were produced from recombinant plasmid pVD2, expressing the prM, 80% and 20% COOH terminus of the envelope proteins of DENV-2 (Asian 1 genotype, strain 16681) and Japanese encephalitis virus (strain SA14-14-2), respectively NCBI-ID: 11060 / Sci species name: dengue virus serotype 2 / Sci species strain: 16681 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: Yes / Virus empty: Yes |
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Host (natural) | Organism: Aedes aegypti mosquitoes |
Host system | Organism: ![]() |
Virus shell | Shell ID: 1 / Name: glycoprotein E and M / Diameter: 60.0 Å / T number (triangulation number): 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL | ||||||||
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Buffer | pH: 7.4 Component:
Details: Solutions were made fresh to avoid contamination | ||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 87 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 / Details: blot for 3 seconds before plunging. | ||||||||
Details | the sample was monodisperse |
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Electron microscopy
Microscope | JEOL 2100F |
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Image recording | Film or detector model: DIRECT ELECTRON DE-12 (4k x 3k) / Detector mode: COUNTING / Average electron dose: 10.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |
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