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- EMDB-28022: Adeno-associated virus type 2 VLP displaying M2 peptide -

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Basic information

Entry
Database: EMDB / ID: EMD-28022
TitleAdeno-associated virus type 2 VLP displaying M2 peptide
Map datamap
Sample
  • Virus: adeno-associated virus 2
KeywordsMimotopes / Dengue / Zika / VIRUS LIKE PARTICLE
Biological speciesadeno-associated virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsHernandez C / Kopylov M
Funding support United States, 1 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
CitationJournal: Biotechnol Bioeng / Year: 2023
Title: Mimotope discovery as a tool to design a vaccine against Zika and dengue viruses.
Authors: Esmeralda Cuevas-Juárez / Arturo Liñan-Torres / Carolina Hernández / Mykhailo Kopylov / Clint S Potter / Bridget Carragher / Octavio T Ramírez / Laura A Palomares /
Abstract: Vaccine development against dengue virus is challenging because of the antibody-dependent enhancement of infection (ADE), which causes severe disease. Consecutive infections by Zika (ZIKV) and/or ...Vaccine development against dengue virus is challenging because of the antibody-dependent enhancement of infection (ADE), which causes severe disease. Consecutive infections by Zika (ZIKV) and/or dengue viruses (DENV), or vaccination can predispose to ADE. Current vaccines and vaccine candidates contain the complete envelope viral protein, with epitopes that can raise antibodies causing ADE. We used the envelope dimer epitope (EDE), which induces neutralizing antibodies that do not elicit ADE, to design a vaccine against both flaviviruses. However, EDE is a discontinuous quaternary epitope that cannot be isolated from the E protein without other epitopes. Utilizing phage display, we selected three peptides that mimic the EDE. Free mimotopes were disordered and did not elicit an immune response. After their display on adeno-associated virus (AAV) capsids (VLP), they recovered their structure and were recognized by an EDE-specific antibody. Characterization by cryo-EM and enzyme-linked immunosorbent assay confirmed the correct display of a mimotope on the surface of the AAV VLP and its recognition by the specific antibody. Immunization with the AAV VLP displaying one of the mimotopes induced antibodies that recognized ZIKV and DENV. This work provides the basis for developing a Zika and dengue virus vaccine candidate that will not induce ADE.
History
DepositionSep 2, 2022-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateSep 13, 2023-
Current statusSep 13, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28022.png

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Map

FileDownload / File: emd_28022.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Voxel sizeX=Y=Z: 1.083 Å
Density
Contour LevelBy AUTHOR: 0.806
Minimum - Maximum-0.65733993 - 1.9144202
Average (Standard dev.)0.007315665 (±0.13971984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 433.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28022_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: sharp map

Fileemd_28022_additional_1.map
Annotationsharp map
Projections & Slices
AxesZYX

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Histogram

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Half map: half map A

Fileemd_28022_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_28022_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Sample components

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Entire : adeno-associated virus 2

EntireName: adeno-associated virus 2
Components
  • Virus: adeno-associated virus 2

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Supramolecule #1: adeno-associated virus 2

SupramoleculeName: adeno-associated virus 2 / type: virus / ID: 1 / Parent: 0
Details: Produced using the Baculovirus expression vector system and the particles were purified from the cellular pellet using an iodixanol gradient
NCBI-ID: 10804 / Sci species name: adeno-associated virus 2 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes

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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

Concentration1.0 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1935 / Average exposure time: 2.0 sec. / Average electron dose: 47.77 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1141051
Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 2 / Resolution.type: BY AUTHOR / Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33455
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6uov

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