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Yorodumi- EMDB-6341: Electron cryo-microscopy EBV gp350-based encapsulin nanoparticle -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6341 | |||||||||
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Title | Electron cryo-microscopy EBV gp350-based encapsulin nanoparticle | |||||||||
Map data | Reconstruction of EBV gp350-based encapsulin nanoparticle | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 35.0 Å | |||||||||
Authors | Kanekiyo 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 | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6341.map.gz | 13.8 MB | EMDB map data format | |
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Header (meta data) | emd-6341-v30.xml emd-6341.xml | 7.8 KB 7.8 KB | Display Display | EMDB header |
Images | 400_6341.gif 80_6341.gif | 56.9 KB 4.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6341 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6341 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6341.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of EBV gp350-based encapsulin nanoparticle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.019 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : EBV gp350-based encapsulin nanoparticle
Entire | Name: EBV gp350-based encapsulin nanoparticle |
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Components |
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-Supramolecule #1000: EBV gp350-based encapsulin nanoparticle
Supramolecule | Name: EBV gp350-based encapsulin nanoparticle / type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: EBV gp350-based encapsulin nanoparticle
Macromolecule | Name: EBV gp350-based encapsulin nanoparticle / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3 |
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-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: DARK FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Date | Nov 20, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: OTHER / Number images used: 1000 |
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