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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: EMD-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.
Sample
  • Virus: dengue virus serotype 2
Biological speciesdengue virus serotype 2
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
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 / ...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
DepositionMar 2, 2018-
Header (metadata) releaseNov 21, 2018-
Map releaseNov 21, 2018-
UpdateNov 21, 2018-
Current statusNov 21, 2018Processing site: PDBj / Status: Released

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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

FileDownload / File: emd_6926.map.gz / Format: CCP4 / Size: 4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe 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 sizeX=Y=Z: 4 Å
Density
Contour LevelBy AUTHOR: 72. / Movie #1: 72
Minimum - Maximum0. - 127.540000000000006
Average (Standard dev.)50.500480000000003 (±14.068339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions12812864
Spacing12812864
CellA: 512.0 Å / B: 512.0 Å / C: 256.0 Å
α=β=γ: 90.0 °

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
Components
  • Virus: dengue virus serotype 2

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Supramolecule #1: dengue virus serotype 2

SupramoleculeName: 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 systemOrganism: Chlorocebus aethiops (grivet)
Virus shellShell ID: 1 / Name: glycoprotein E and M / Diameter: 60.0 Å / T number (triangulation number): 3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormula
50.0 mMTris-HClTris
100.0 mMNaClSodium chloride
0.1 mMEDTAEthylenediaminetetraacetic acid

Details: Solutions were made fresh to avoid contamination
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 87 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 / Details: blot for 3 seconds before plunging.
Detailsthe sample was monodisperse

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Electron microscopy

MicroscopeJEOL 2100F
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: DIRECT ELECTRON DE-12 (4k x 3k) / Detector mode: COUNTING / Average electron dose: 10.0 e/Å2

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Image processing

Particle selectionNumber selected: 13514
CTF correctionSoftware - Name: EMAN2 (ver. 2)
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN2 (ver. 2)
Final 3D classificationSoftware - Name: EMAN2 (ver. 2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN2 (ver. 2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 (ver. 2) / Number images used: 4217

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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