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- EMDB-32088: Computational design of a potent Epstein-Barr virus fusion protei... -
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Open data
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Basic information
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Title | Computational design of a potent Epstein-Barr virus fusion protein gB nanoparticle vaccine | |||||||||
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![]() | Virology / Microbiology / Vaccine / EBV / IMMUNE SYSTEM | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Sun C / Fang XY / Wang AJ / Liu Z / Zeng MS | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 307.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.4 KB 12.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.1 KB | Display | ![]() |
Images | ![]() | 115 KB | ||
Masks | ![]() | 325 MB | ![]() | |
Filedesc metadata | ![]() | 4.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 625.9 KB | Display | ![]() |
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Full document | ![]() | 625.5 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.374 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : I53-50 NP
Entire | Name: I53-50 NP |
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Components |
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-Supramolecule #1: I53-50 NP
Supramolecule | Name: I53-50 NP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: I53-50A1
Macromolecule | Name: I53-50A1 / type: other / ID: 1 / Classification: other |
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Sequence | String: MNQHSHKDHE TVRIAVVRAR WHAEIVDACV SAFEAAMRDI GGDRFAVDVF DVPGAYEIPL HARTLAETGR YGAVLGTAFV VNGGIYRHEF VASAVINGMM NVQLNTGVPV LSAVLTPHNY DKSKAHTLLF LALFAVKGME AARACVEILA AREKIAAGSL E |
-Macromolecule #2: I53-50B4.PT1
Macromolecule | Name: I53-50B4.PT1 / type: other / ID: 2 / Classification: other |
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Sequence | String: MNQHSHKDHE TVRIAVVRAR WHAEIVDACV SAFEAAMRDI GGDRFAVDVF DVPGAYEIPL HARTLAETGR YGAVLGTAFV VNGGIYRHEF VASAVINGMM NVQLNTGVPV LSAVLTPHNY DKSKAHTLLF LALFAVKGME AARACVEILA AREKIAAGSL E |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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