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Yorodumi- EMDB-32356: Computational design of a potent Epstein-Barr virus fusion protei... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32356 | |||||||||
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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 gammaherpesvirus 4 (Epstein-Barr virus) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 9.33 Å | |||||||||
Authors | Sun C / Wang AJ / Fang XY / Gao YZ / 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_32356.map.gz | 917.9 KB | EMDB map data format | |
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Header (meta data) | emd-32356-v30.xml emd-32356.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32356_fsc.xml | 33.8 KB | Display | FSC data file |
Images | emd_32356.png | 37.6 KB | ||
Filedesc metadata | emd-32356.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32356 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32356 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32356.map.gz / Format: CCP4 / Size: 8.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 2.668 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : gB-I53-50 NP
Entire | Name: gB-I53-50 NP |
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Components |
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-Supramolecule #1: gB-I53-50 NP
Supramolecule | Name: gB-I53-50 NP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Human gammaherpesvirus 4 (Epstein-Barr virus) |
-Macromolecule #1: glycoprotein B
Macromolecule | Name: glycoprotein B / type: other / ID: 1 / Classification: other |
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Source (natural) | Organism: Human gammaherpesvirus 4 (Epstein-Barr virus) |
Sequence | String: QTPEQPAPPA TTVQPTATRQ QTSFPFRVCE LSSHGDLFRF SSDIQCPSFG TRENHTEGLL MVFKDNIIPY SFKVRSYTKI VTNILIYNGH RADSVTNRHE EKFSVESYET DQMDTIYQCY NAVKMTKDGL TRVYVDRDGV NITVNLKPTG GLANGVRRYA SQTELYDAPG ...String: QTPEQPAPPA TTVQPTATRQ QTSFPFRVCE LSSHGDLFRF SSDIQCPSFG TRENHTEGLL MVFKDNIIPY SFKVRSYTKI VTNILIYNGH RADSVTNRHE EKFSVESYET DQMDTIYQCY NAVKMTKDGL TRVYVDRDGV NITVNLKPTG GLANGVRRYA SQTELYDAPG RVEATYRTRT TVNCLITDMM AKSNSPFDFF VTTTGQTVEM SPFYDGKNTE TFHERADSFH VRTNYKIVDY DNRGTNPQGE RRAFLDKGTY TLSWKLENRT AYCPLQHWQT FDSTIATETG KSIHFVTDEG TSSFVTNTTV GIELPDAFKC IEEQVNKTMH EKYEAVQDRY TKGQEAITYF ITSGGLLLAW LPLTPRSLAT VKNLTELTTP TSSPPSSPSP PAPPAARGST SAAVLRRRRR NAGNATTPVP PAAPGKSLGT LNNPATVQIQ FAYDSLRRQI NRMLGDLARA WCLEQKRQNM VLRELTKINP TTVMSSIYGK AVAAKRLGDV ISVSQCVPVN QATVTLRKSM RVPGSETMCY SRPLVSFSFI NDTKTYEGQL GTDNEIFLTK KMTEVCQATS QYYFQSGNEI HVYNDYHHFK TIELDGIATL QTFISLNTSL IENIDFASLE LYSRDEQRAS NVFDLEGIFR EYNFQAQNIA GLRKDLDNAV S |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-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: 1.0 µm / Nominal magnification: 53000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 2.44 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |