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- EMDB-6341: Electron cryo-microscopy EBV gp350-based encapsulin nanoparticle -

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Basic information

Entry
Database: EMDB / ID: EMD-6341
TitleElectron cryo-microscopy EBV gp350-based encapsulin nanoparticle
Map dataReconstruction of EBV gp350-based encapsulin nanoparticle
Sample
  • Sample: EBV gp350-based encapsulin nanoparticle
  • Protein or peptide: EBV gp350-based encapsulin nanoparticle
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 35.0 Å
AuthorsKanekiyo M / Bu W / Joyce MG / Meng G / Whittle JR / Baxa U / Yamamoto T / Narpala S / Todd JP / Rao SS ...Kanekiyo M / Bu W / Joyce MG / Meng G / Whittle JR / Baxa U / Yamamoto T / Narpala S / Todd JP / Rao SS / McDermott AB / Koup RA / Rossmann MG / Mascola JR / Graham BS / Cohen JI / Nabel GJ
CitationJournal: Cell / Year: 2015
Title: Rational Design of an Epstein-Barr Virus Vaccine Targeting the Receptor-Binding Site.
Authors: Masaru Kanekiyo / Wei Bu / M Gordon Joyce / Geng Meng / James R R Whittle / Ulrich Baxa / Takuya Yamamoto / Sandeep Narpala / John-Paul Todd / Srinivas S Rao / Adrian B McDermott / Richard A ...Authors: Masaru Kanekiyo / Wei Bu / M Gordon Joyce / Geng Meng / James R R Whittle / Ulrich Baxa / Takuya Yamamoto / Sandeep Narpala / John-Paul Todd / Srinivas S Rao / Adrian B McDermott / Richard A Koup / Michael G Rossmann / John R Mascola / Barney S Graham / Jeffrey I Cohen / Gary J Nabel /
Abstract: Epstein-Barr virus (EBV) represents a major global health problem. Though it is associated with infectious mononucleosis and ∼200,000 cancers annually worldwide, a vaccine is not available. The ...Epstein-Barr virus (EBV) represents a major global health problem. Though it is associated with infectious mononucleosis and ∼200,000 cancers annually worldwide, a vaccine is not available. The major target of immunity is EBV glycoprotein 350/220 (gp350) that mediates attachment to B cells through complement receptor 2 (CR2/CD21). Here, we created self-assembling nanoparticles that displayed different domains of gp350 in a symmetric array. By focusing presentation of the CR2-binding domain on nanoparticles, potent neutralizing antibodies were elicited in mice and non-human primates. The structurally designed nanoparticle vaccine increased neutralization 10- to 100-fold compared to soluble gp350 by targeting a functionally conserved site of vulnerability, improving vaccine-induced protection in a mouse model. This rational approach to EBV vaccine design elicited potent neutralizing antibody responses by arrayed presentation of a conserved viral entry domain, a strategy that can be applied to other viruses.
History
DepositionMay 25, 2015-
Header (metadata) releaseJun 3, 2015-
Map releaseMay 4, 2016-
UpdateMay 4, 2016-
Current statusMay 4, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6341.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of EBV gp350-based encapsulin nanoparticle
Voxel sizeX=Y=Z: 3.019 Å
Density
Contour LevelBy EMDB: 11.0 / Movie #1: 6
Minimum - Maximum-4.44930649 - 283.391113280000013
Average (Standard dev.)9.26027489 (±36.378257750000003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 483.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.0193.0193.019
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z483.040483.040483.040
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-31-64
NX/NY/NZ6963129
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-4.449283.3919.260

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Supplemental data

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Sample components

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Entire : EBV gp350-based encapsulin nanoparticle

EntireName: EBV gp350-based encapsulin nanoparticle
Components
  • Sample: EBV gp350-based encapsulin nanoparticle
  • Protein or peptide: EBV gp350-based encapsulin nanoparticle

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Supramolecule #1000: EBV gp350-based encapsulin nanoparticle

SupramoleculeName: EBV gp350-based encapsulin nanoparticle / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: EBV gp350-based encapsulin nanoparticle

MacromoleculeName: EBV gp350-based encapsulin nanoparticle / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human

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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

VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateNov 20, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: OTHER / Number images used: 1000

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