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- EMDB-32356: Computational design of a potent Epstein-Barr virus fusion protei... -

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Basic information

Entry
Database: EMDB / ID: EMD-32356
TitleComputational design of a potent Epstein-Barr virus fusion protein gB nanoparticle vaccine
Map data
Sample
  • Complex: gB-I53-50 NP
    • Other: glycoprotein B
KeywordsVirology / Microbiology / Vaccine / EBV / IMMUNE SYSTEM
Biological speciesHuman gammaherpesvirus 4 (Epstein-Barr virus)
Methodsubtomogram averaging / cryo EM / Resolution: 9.33 Å
AuthorsSun C / Wang AJ / Fang XY / Gao YZ / 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
DepositionDec 7, 2021-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateJan 3, 2024-
Current statusJan 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32356.png

Downloads & links

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Map

FileDownload / File: emd_32356.map.gz / Format: CCP4 / Size: 8.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.67 Å/pix.
x 132 pix.
= 352.176 Å		2.67 Å/pix.
x 132 pix.
= 352.176 Å		2.67 Å/pix.
x 132 pix.
= 352.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.03
Minimum - Maximum-2.495635 - 20.055810000000001
Average (Standard dev.)0.10924888 (±0.9853499)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions132132132
Spacing132132132
CellA=B=C: 352.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : gB-I53-50 NP

EntireName: gB-I53-50 NP
Components
  • Complex: gB-I53-50 NP
    • Other: glycoprotein B

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Supramolecule #1: gB-I53-50 NP

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

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Macromolecule #1: glycoprotein B

MacromoleculeName: glycoprotein B / type: other / ID: 1 / Classification: other
Source (natural)Organism: Human gammaherpesvirus 4 (Epstein-Barr virus)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 2.44 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: 1.0 µm / Nominal magnification: 53000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 18173
ExtractionNumber tomograms: 78 / Number images used: 42640
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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