[English] 日本語
Yorodumi- EMDB-6926: CryoEM structure of mature dengue virus-like particle at 13 Angst... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6926 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of mature dengue virus-like particle at 13 Angstroms resolution | |||||||||
Map data | 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. | |||||||||
Sample |
| |||||||||
Biological species | dengue virus serotype 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.0 Å | |||||||||
Authors | Wu SR / Chao DY | |||||||||
Citation | Journal: Elife / Year: 2018 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6926.map.gz | 1.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6926-v30.xml emd-6926.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_6926.png | 125.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6926 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6926 | HTTPS FTP |
-Validation report
Summary document | emd_6926_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6926_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_6926_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6926 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6926 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_6926.map.gz / Format: CCP4 / Size: 4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : dengue virus serotype 2
Entire | Name: dengue virus serotype 2 |
---|---|
Components |
|
-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 |
---|---|
Host (natural) | Organism: Aedes aegypti mosquitoes |
Host system | Organism: Chlorocebus aethiops (grivet) |
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 |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | ||||||||
---|---|---|---|---|---|---|---|---|---|
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 |
-Electron microscopy
Microscope | JEOL 2100F |
---|---|
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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |
---|