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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: 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. |
![]() | dengue virus serotype 2: virus ![]() |
Source | ![]() ![]() ![]() |
Method | ![]() ![]() |
![]() | Wu SR / Chao DY |
![]() | Journal: Elife / Year: 2018 Title: Epitope resurfacing on dengue virus-like particle vaccine preparation to induce broad neutralizing antibody. ![]() |
Date | Deposition: Mar 2, 2018 / Header (metadata) release: Nov 21, 2018 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
![]() | ![]() |
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Header (meta data in XML format) | ![]() ![]() ![]() |
Images | ![]() |
FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6926 |
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Links
-Related structure data
Similar-shape strucutres |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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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: dengue virus serotype 2 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 Number of components: 1 |
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-Component #1: virus, dengue virus serotype 2
Virus | Name: dengue virus serotype 2 / Class: VIRUS-LIKE PARTICLE 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 Empty: Yes / Enveloped: Yes / Isolate: SEROTYPE |
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Species | Species: ![]() ![]() ![]() |
Source (engineered) | Expression System: ![]() ![]() |
Source (natural) | Host Species: Aedes aegypti mosquitoes |
Shell #1 | Name of element: glycoprotein E and M / Diameter: 60.0 Å / T number(triangulation number): 3 |
-Experimental details
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Sample preparation
Specimen | Specimen state: particle / Method: ![]() |
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Sample solution | Specimen conc.: 0.1 mg/ml Buffer solution: Solutions were made fresh to avoid contamination pH: 7.4 |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 87 % / Details: blot for 3 seconds before plunging. |
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Electron microscopy imaging
![]() | Microscope: JEOL 2100F |
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Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: OTHER |
Camera | Detector: DIRECT ELECTRON DE-12 (4k x 3k) |
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Image processing
![]() | Method: ![]() |
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3D reconstruction | Software: EMAN2 / Resolution: 13 Å / Resolution method: FSC 0.5 CUT-OFF |
-Atomic model buiding
Modeling #1 | Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL |
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