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Yorodumi- EMDB-6529: Negative stain EM reconstruction of Bundibugyo virus (BDBV) glyco... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6529 | |||||||||
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Title | Negative stain EM reconstruction of Bundibugyo virus (BDBV) glycoprotein in complex with a human IgG1 Fab | |||||||||
Map data | Reconstruction of Fab of human monoclonal antibody BDBV432 in complex with mucin-deleted Bundibugyo virus glycoprotein | |||||||||
Sample |
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Keywords | Ebola virus / EBOV / GP / antibody / Bundibugyo virus / BDBV / Fab | |||||||||
Biological species | Homo sapiens (human) / Ebola virus sp. | |||||||||
Method | single particle reconstruction / Resolution: 17.0 Å | |||||||||
Authors | Flyak AI / Shen X / Murin CD / Turner HL / Fusco ML / Lampley R / Kose N / Ilinykh PA / Kuzmina N / Branchizio A ...Flyak AI / Shen X / Murin CD / Turner HL / Fusco ML / Lampley R / Kose N / Ilinykh PA / Kuzmina N / Branchizio A / King H / Brown L / Davidson E / Doranz BJ / Slaughter JC / Sapparapu G / Klages C / Ksiazek TG / Saphire EO / Ward AB / Bukreyev A / Crowe JE | |||||||||
Citation | Journal: Cell / Year: 2016 Title: Cross-Reactive and Potent Neutralizing Antibody Responses in Human Survivors of Natural Ebolavirus Infection. Authors: Andrew I Flyak / Xiaoli Shen / Charles D Murin / Hannah L Turner / Joshua A David / Marnie L Fusco / Rebecca Lampley / Nurgun Kose / Philipp A Ilinykh / Natalia Kuzmina / Andre Branchizio / ...Authors: Andrew I Flyak / Xiaoli Shen / Charles D Murin / Hannah L Turner / Joshua A David / Marnie L Fusco / Rebecca Lampley / Nurgun Kose / Philipp A Ilinykh / Natalia Kuzmina / Andre Branchizio / Hannah King / Leland Brown / Christopher Bryan / Edgar Davidson / Benjamin J Doranz / James C Slaughter / Gopal Sapparapu / Curtis Klages / Thomas G Ksiazek / Erica Ollmann Saphire / Andrew B Ward / Alexander Bukreyev / James E Crowe / Abstract: Recent studies have suggested that antibody-mediated protection against the Ebolaviruses may be achievable, but little is known about whether or not antibodies can confer cross-reactive protection ...Recent studies have suggested that antibody-mediated protection against the Ebolaviruses may be achievable, but little is known about whether or not antibodies can confer cross-reactive protection against viruses belonging to diverse Ebolavirus species, such as Ebola virus (EBOV), Sudan virus (SUDV), and Bundibugyo virus (BDBV). We isolated a large panel of human monoclonal antibodies (mAbs) against BDBV glycoprotein (GP) using peripheral blood B cells from survivors of the 2007 BDBV outbreak in Uganda. We determined that a large proportion of mAbs with potent neutralizing activity against BDBV bind to the glycan cap and recognize diverse epitopes within this major antigenic site. We identified several glycan cap-specific mAbs that neutralized multiple ebolaviruses, including SUDV, and a cross-reactive mAb that completely protected guinea pigs from the lethal challenge with heterologous EBOV. Our results provide a roadmap to develop a single antibody-based treatment effective against multiple Ebolavirus infections. | |||||||||
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_6529.map.gz | 1.8 MB | EMDB map data format | |
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Header (meta data) | emd-6529-v30.xml emd-6529.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_6529.jpg | 468.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6529 | HTTPS FTP |
-Validation report
Summary document | emd_6529_validation.pdf.gz | 79 KB | Display | EMDB validaton report |
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Full document | emd_6529_full_validation.pdf.gz | 78.1 KB | Display | |
Data in XML | emd_6529_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6529 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6529 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6529.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Fab of human monoclonal antibody BDBV432 in complex with mucin-deleted Bundibugyo virus glycoprotein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.1 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 : Fab fragment of BDBV432 human IgG1 monoclonal antibody to Bundibu...
Entire | Name: Fab fragment of BDBV432 human IgG1 monoclonal antibody to Bundibugyo virus in complex with mucin-deleted Bundibugyo virus GP |
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Components |
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-Supramolecule #1000: Fab fragment of BDBV432 human IgG1 monoclonal antibody to Bundibu...
Supramolecule | Name: Fab fragment of BDBV432 human IgG1 monoclonal antibody to Bundibugyo virus in complex with mucin-deleted Bundibugyo virus GP type: sample / ID: 1000 Oligomeric state: Three Fabs (each consisting of one heavy chain and one light chain) bind to a single GP (consisting of a trimer of heterodimers of GP1 and GP2) Number unique components: 2 |
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Molecular weight | Theoretical: 310 KDa |
-Macromolecule #1: human IgG1 monoclonal antibody Fab
Macromolecule | Name: human IgG1 monoclonal antibody Fab / type: protein_or_peptide / ID: 1 / Name.synonym: Fab Details: Fabs were generated by optimized papain proteolysis of IgG1. There are three Fabs bound to each trimeric GP. Number of copies: 3 Oligomeric state: heterodimer (one heavy chain, one light chain) Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: Peripheral blood mononuclear cells |
Molecular weight | Theoretical: 50 KDa |
-Macromolecule #2: Bundibugyo virus glycoprotein, mucin-deleted
Macromolecule | Name: Bundibugyo virus glycoprotein, mucin-deleted / type: protein_or_peptide / ID: 2 / Name.synonym: BDBV GPdMuc Details: Recombinantly expressed ectodomain of Bundibugyo virus GP. Mucin-like domains were deleted from the expression construct, as were the transmembrane domains and cytoplasmic tail. Number of copies: 1 Oligomeric state: trimer of heterodimers (consisting of covalently linked GP1 and GP2) Recombinant expression: Yes |
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Source (natural) | Organism: Ebola virus sp. / Strain: Bundibugyo virus |
Molecular weight | Theoretical: 160 KDa |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) / Recombinant cell: S2 / Recombinant plasmid: pMT puro |
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL |
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Buffer | pH: 7.4 / Details: 20 mM Tris, 150 mM NaCl |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Date | Mar 5, 2015 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 73 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 12008 |
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