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Yorodumi- EMDB-32088: Computational design of a potent Epstein-Barr virus fusion protei... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32088 | |||||||||
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Title | Computational design of a potent Epstein-Barr virus fusion protein gB nanoparticle vaccine | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Virology / Microbiology / Vaccine / EBV / IMMUNE SYSTEM | |||||||||
Biological species | Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Sun C / Fang XY / Wang AJ / Liu Z / Zeng MS | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32088.map.gz | 307.1 MB | EMDB map data format | |
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Header (meta data) | emd-32088-v30.xml emd-32088.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32088_fsc.xml | 17.1 KB | Display | FSC data file |
Images | emd_32088.png | 115 KB | ||
Masks | emd_32088_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-32088.cif.gz | 4.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32088 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32088 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32088.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_32088_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) |
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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