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- EMDB-14863: Bacteriophage T5 head - pb10-N-Ter fused to OVA -

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Basic information

Entry
Database: EMDB / ID: EMD-14863
TitleBacteriophage T5 head - pb10-N-Ter fused to OVA
Map dataTo visualize T5 please use 0.0279 contour level To visualize T5 OVA please use 0.0039
Sample
  • Virus: Escherichia phage T5 (virus)
KeywordsBacteriophage head Antigen OVA / VIRUS
Biological speciesEscherichia phage T5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsSchoehn G / Boulanger P / Benihoud K
Funding support France, 1 items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-02 France
CitationJournal: NPJ Vaccines / Year: 2024
Title: Antigen self-anchoring onto bacteriophage T5 capsid-like particles for vaccine design.
Authors: Emeline Vernhes / Linda Larbi Chérif / Nicolas Ducrot / Clément Vanbergue / Malika Ouldali / Lena Zig / N'diaye Sidibe / Sylviane Hoos / Luis Ramirez-Chamorro / Madalena Renouard / ...Authors: Emeline Vernhes / Linda Larbi Chérif / Nicolas Ducrot / Clément Vanbergue / Malika Ouldali / Lena Zig / N'diaye Sidibe / Sylviane Hoos / Luis Ramirez-Chamorro / Madalena Renouard / Ombeline Rossier / Patrick England / Guy Schoehn / Pascale Boulanger / Karim Benihoud /
Abstract: The promises of vaccines based on virus-like particles stimulate demand for universal non-infectious virus-like platforms that can be efficiently grafted with large antigens. Here, we harnessed the ...The promises of vaccines based on virus-like particles stimulate demand for universal non-infectious virus-like platforms that can be efficiently grafted with large antigens. Here, we harnessed the modularity and extreme affinity of the decoration protein pb10 for the capsid of bacteriophage T5. SPR experiments demonstrated that pb10 fused to mCherry or to the model antigen ovalbumin (Ova) retained picomolar affinity for DNA-free T5 capsid-like particles (T5-CLPs), while cryo-EM studies attested to the full occupancy of the 120 capsid binding sites. Mice immunization with CLP-bound pb10-Ova chimeras elicited strong long-lasting anti-Ova humoral responses involving a large panel of isotypes, as well as CD8 T cell responses, without any extrinsic adjuvant. Therefore, T5-CLP constitutes a unique DNA-free bacteriophage capsid able to display a regular array of large antigens through highly efficient chemical-free anchoring. Its ability to elicit robust immune responses paves the way for further development of this novel vaccination platform.
History
DepositionApr 28, 2022-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14863.png

Downloads & links

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Map

FileDownload / File: emd_14863.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTo visualize T5 please use 0.0279 contour level To visualize T5 OVA please use 0.0039
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.9 Å/pix.
x 420 pix.
= 1218. Å		2.9 Å/pix.
x 420 pix.
= 1218. Å		2.9 Å/pix.
x 420 pix.
= 1218. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0039
Minimum - Maximum-0.011991504 - 0.060132075
Average (Standard dev.)0.000060447917 (±0.004804779)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 1218.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14863_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14863_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage T5

EntireName: Escherichia phage T5 (virus)
Components
  • Virus: Escherichia phage T5 (virus)

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Supramolecule #1: Escherichia phage T5

SupramoleculeName: Escherichia phage T5 / type: virus / ID: 1 / Parent: 0 / Details: E coli; double mutant / NCBI-ID: 2695836 / Sci species name: Escherichia phage T5 / Virus type: VIRION / Virus isolate: OTHER / 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 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-40 / Number grids imaged: 1 / Number real images: 2500 / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 12000
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 10449
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 3 / Software - Name: RELION
FSC plot (resolution estimation)

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