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- EMDB-6531: Negative stain EM reconstruction of Bundibugyo virus (BDBV) glyco... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6531 | |||||||||
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Title | Negative stain EM reconstruction of Bundibugyo virus (BDBV) glycoprotein in complex with a human IgG1 Fab | |||||||||
![]() | Reconstruction of Bundibugyo virus (BDBV) glycoprotein (GP) ectodomain (missing transmembrane and cytoplasmic tail, GPdTM) in complex with Fab of BDBV353 human IgG1 | |||||||||
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![]() | Ebola virus / EBOV / GP / antibody / Bundibugyo virus / BDBV / Fab | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / Resolution: 25.0 Å | |||||||||
![]() | 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 | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.8 KB 11.8 KB | Display Display | ![]() |
Images | ![]() | 76.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Reconstruction of Bundibugyo virus (BDBV) glycoprotein (GP) ectodomain (missing transmembrane and cytoplasmic tail, GPdTM) in complex with Fab of BDBV353 human IgG1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : Bundibugyo virus (BDBV) glycoprotein (GP) ectodomain (missing tra...
Entire | Name: Bundibugyo virus (BDBV) glycoprotein (GP) ectodomain (missing transmembrane and cytoplasmic tail, GPdTM) in complex with Fab of BDBV353 human IgG1 |
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Components |
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-Supramolecule #1000: Bundibugyo virus (BDBV) glycoprotein (GP) ectodomain (missing tra...
Supramolecule | Name: Bundibugyo virus (BDBV) glycoprotein (GP) ectodomain (missing transmembrane and cytoplasmic tail, GPdTM) in complex with Fab of BDBV353 human IgG1 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: 360 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: ![]() |
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 GPdTM 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: ![]() |
Molecular weight | Theoretical: 210 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
![]() | single particle reconstruction |
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Aggregation state | particle |
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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 |
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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: 76 |
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 |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 8418 |
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