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- EMDB-8424: Chikungunya virus-like particle inserted with circumsporozoite pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-8424
TitleChikungunya virus-like particle inserted with circumsporozoite protein peptides of Plasmodium falciparum
Map dataChikungunya virus-like particle inserted with circumsporozoite protein peptides of Plasmodium falciparum
Sample
  • Virus: Chikungunya virus strain Senegal 37997
Biological speciesChikungunya virus strain Senegal 37997
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsYap ML / Urakami A / Sakurai A / Ishikawa M / Rossmann MG / Akahata W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesR01 AI095366 United States
CitationJournal: Clin Vaccine Immunol / Year: 2017
Title: Development of a Novel Virus-Like Particle Vaccine Platform That Mimics the Immature Form of Alphavirus.
Authors: Akane Urakami / Atsuko Sakurai / Momoko Ishikawa / Moh Lan Yap / Yevel Flores-Garcia / Yasunari Haseda / Taiki Aoshi / Fidel P Zavala / Michael G Rossmann / Sachiko Kuno / Ryuji Ueno / Wataru Akahata /
Abstract: Virus-like particles (VLPs) are noninfectious multiprotein structures that are engineered to self-assemble from viral structural proteins. Here, we developed a novel VLP-based vaccine platform ...Virus-like particles (VLPs) are noninfectious multiprotein structures that are engineered to self-assemble from viral structural proteins. Here, we developed a novel VLP-based vaccine platform utilizing VLPs from the chikungunya virus. We identified two regions within the envelope protein, a structural component of chikungunya, where foreign antigens can be inserted without compromising VLP structure. Our VLP displays 480 copious copies of an inserted antigen on the VLP surface in a highly symmetric manner and is thus capable of inducing strong immune responses against any inserted antigen. Furthermore, by mimicking the structure of the immature form of the virus, we altered our VLP's dynamics and enhanced its immunogenicity. We used the circumsporozoite protein (CSP) of the malaria parasite as an antigen and demonstrated that our VLP-based vaccine elicits strong immune responses against CSP in animals. The sera from immunized monkeys protected mice from malaria infection. Likewise, mice vaccinated with CSP-containing VLPs were protected from an infectious sporozoite challenge. Hence, our uniquely engineered VLP platform can serve as a blueprint for the development of vaccines against other pathogens and diseases.
History
DepositionOct 6, 2016-
Header (metadata) releaseOct 19, 2016-
Map releaseFeb 21, 2018-
UpdateSep 4, 2019-
Current statusSep 4, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_8424.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChikungunya virus-like particle inserted with circumsporozoite protein peptides of Plasmodium falciparum
Voxel sizeX=Y=Z: 2.6 Å
Density
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-2.790695 - 5.755798
Average (Standard dev.)0.0015732318 (±0.36349502)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-176-176-176
Dimensions352352352
Spacing352352352
CellA=B=C: 915.19995 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.62.62.6
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z915.200915.200915.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-2600
NX/NY/NZ264044
MAP C/R/S123
start NC/NR/NS-176-176-176
NC/NR/NS352352352
D min/max/mean-2.7915.7560.002

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Supplemental data

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Sample components

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Entire : Chikungunya virus strain Senegal 37997

EntireName: Chikungunya virus strain Senegal 37997
Components
  • Virus: Chikungunya virus strain Senegal 37997

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Supramolecule #1: Chikungunya virus strain Senegal 37997

SupramoleculeName: Chikungunya virus strain Senegal 37997 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 371095 / Sci species name: Chikungunya virus strain Senegal 37997 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host systemOrganism: Homo sapiens (human) / Recombinant cell: Human embryonic kidney / Recombinant plasmid: pUC59

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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

Concentration3 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 36.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 2840
FSC plot (resolution estimation)

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