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- EMDB-6926: CryoEM structure of mature dengue virus-like particle at 13 Angst... -

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Basic information

Entry
Database: EMDB / ID: 6926
TitleCryoEM structure of mature dengue virus-like particle at 13 Angstroms resolution
Map dataThe single particle cryo-EM reconstruction of highly matured virus-like particles derived from DENV serotype 2 (mD2VLP). The images analyses were performed using EMAN2.
Sampledengue virus serotype 2:
virus
Sourcedengue virus serotype 2
Methodsingle particle reconstruction / cryo EM / 13 Å resolution
AuthorsWu SR / Chao DY
CitationJournal: 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 / Sheng-Ren Chen / Shang-Rung Wu / Day-Yu Chao
DateDeposition: 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
  • Surface view with section colored by density value
  • Surface level: 72
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 72
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6926.png

Downloads & links

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Map

Fileemd_6926.map.gz (map file in CCP4 format, 4195 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
4 Å/pix.
= 256. Å		128 pix
4 Å/pix.
= 512. Å		128 pix
4 Å/pix.
= 512. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour Level:72.0 (by author), 72 (movie #1):
Minimum - Maximum0.0 - 127.540000000000006
Average (Standard dev.)50.500480000000003 (14.068339)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions12812864
Origin0.00.00.0
Limit127.0127.063.0
Spacing12812864
CellA: 512.0 Å / B: 512.0 Å / C: 256.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z444
M x/y/z12812864
origin x/y/z0.0000.0000.000
length x/y/z512.000512.000256.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS12812864
D min/max/mean0.000127.54050.500

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Supplemental data

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Sample components

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Entire dengue virus serotype 2

EntireName: 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

VirusName: 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
SpeciesSpecies: dengue virus serotype 2 / Strain: 16681
Source (engineered)Expression System: Chlorocebus aethiops (grivet)
Source (natural)Host Species: Aedes aegypti mosquitoes
Shell #1Name of element: glycoprotein E and M / Diameter: 60.0 Å / T number(triangulation number): 3

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/ml
Buffer solution: Solutions were made fresh to avoid contamination
pH: 7.4
VitrificationInstrument: 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

ImagingMicroscope: JEOL 2100F
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: DIRECT ELECTRON DE-12 (4k x 3k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 4217
3D reconstructionSoftware: EMAN2 / Resolution: 13 Å / Resolution method: FSC 0.5 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL

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