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- EMDB-32088: Computational design of a potent Epstein-Barr virus fusion protei... -

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Basic information

Entry
Database: EMDB / ID: EMD-32088
TitleComputational design of a potent Epstein-Barr virus fusion protein gB nanoparticle vaccine
Map data
Sample
  • Complex: I53-50 NP
    • Other: I53-50A1
    • Other: I53-50B4.PT1
KeywordsVirology / Microbiology / Vaccine / EBV / IMMUNE SYSTEM
Biological speciesHuman herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSun C / Fang XY / Wang AJ / Liu Z / Zeng MS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: Cell Host Microbe / Year: 2023
Title: A gB nanoparticle vaccine elicits a protective neutralizing antibody response against EBV
Authors: Sun C / Kang YF / Fang XY / Liu YN / Bu GL / Wang AJ / Li Y / Zhu QY / Zhang H / Xie C / Kong XW / Peng YJ / Lin WJ / Zhou L / Chen XC / Lu ZZ / Xu HQ / Hong DC / Zhang X / Zhong L / Feng GK ...Authors: Sun C / Kang YF / Fang XY / Liu YN / Bu GL / Wang AJ / Li Y / Zhu QY / Zhang H / Xie C / Kong XW / Peng YJ / Lin WJ / Zhou L / Chen XC / Lu ZZ / Xu HQ / Hong DC / Zhang X / Zhong L / Feng GK / Zeng YX / Xu M / Zhong Q / Liu Z / Zeng MS
History
DepositionOct 19, 2021-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateJan 3, 2024-
Current statusJan 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32088.png

Downloads & links

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Map

FileDownload / File: emd_32088.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 440 pix.
= 604.56 Å		1.37 Å/pix.
x 440 pix.
= 604.56 Å		1.37 Å/pix.
x 440 pix.
= 604.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.374 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.725
Minimum - Maximum-2.22307 - 4.5851364
Average (Standard dev.)0.008470717 (±0.12085852)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 604.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32088_msk_1.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 : I53-50 NP

EntireName: I53-50 NP
Components
  • Complex: I53-50 NP
    • Other: I53-50A1
    • Other: I53-50B4.PT1

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Supramolecule #1: I53-50 NP

SupramoleculeName: I53-50 NP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))

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Macromolecule #1: I53-50A1

MacromoleculeName: I53-50A1 / type: other / ID: 1 / Classification: other
SequenceString:
MNQHSHKDHE TVRIAVVRAR WHAEIVDACV SAFEAAMRDI GGDRFAVDVF DVPGAYEIPL HARTLAETGR YGAVLGTAFV VNGGIYRHEF VASAVINGMM NVQLNTGVPV LSAVLTPHNY DKSKAHTLLF LALFAVKGME AARACVEILA AREKIAAGSL E

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Macromolecule #2: I53-50B4.PT1

MacromoleculeName: I53-50B4.PT1 / type: other / ID: 2 / Classification: other
SequenceString:
MNQHSHKDHE TVRIAVVRAR WHAEIVDACV SAFEAAMRDI GGDRFAVDVF DVPGAYEIPL HARTLAETGR YGAVLGTAFV VNGGIYRHEF VASAVINGMM NVQLNTGVPV LSAVLTPHNY DKSKAHTLLF LALFAVKGME AARACVEILA AREKIAAGSL E

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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

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 0-39 / Number real images: 3360 / Average exposure time: 9.6 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 294263
Startup modelType of model: NONE
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1.0) / Number images used: 143279
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Avg.num./class: 47760 / Software - Name: cryoSPARC (ver. 3.1.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER

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