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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7928 | |||||||||
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Title | VIC32 Fab in complex with Ebola virus GP | |||||||||
![]() | VIC32 antibody Fab in complex with Ebola virus GP | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 19.0 Å | |||||||||
![]() | Turner H / Murin CD / Pallesen J / Ward AB | |||||||||
![]() | ![]() Title: Systematic Analysis of Monoclonal Antibodies against Ebola Virus GP Defines Features that Contribute to Protection. Authors: Erica Ollmann Saphire / Sharon L Schendel / Marnie L Fusco / Karthik Gangavarapu / Bronwyn M Gunn / Anna Z Wec / Peter J Halfmann / Jennifer M Brannan / Andrew S Herbert / Xiangguo Qiu / ...Authors: Erica Ollmann Saphire / Sharon L Schendel / Marnie L Fusco / Karthik Gangavarapu / Bronwyn M Gunn / Anna Z Wec / Peter J Halfmann / Jennifer M Brannan / Andrew S Herbert / Xiangguo Qiu / Kshitij Wagh / Shihua He / Elena E Giorgi / James Theiler / Kathleen B J Pommert / Tyler B Krause / Hannah L Turner / Charles D Murin / Jesper Pallesen / Edgar Davidson / Rafi Ahmed / M Javad Aman / Alexander Bukreyev / Dennis R Burton / James E Crowe / Carl W Davis / George Georgiou / Florian Krammer / Christos A Kyratsous / Jonathan R Lai / Cory Nykiforuk / Michael H Pauly / Pramila Rijal / Ayato Takada / Alain R Townsend / Viktor Volchkov / Laura M Walker / Cheng-I Wang / Larry Zeitlin / Benjamin J Doranz / Andrew B Ward / Bette Korber / Gary P Kobinger / Kristian G Andersen / Yoshihiro Kawaoka / Galit Alter / Kartik Chandran / John M Dye / / ![]() ![]() ![]() ![]() ![]() ![]() Abstract: Antibodies are promising post-exposure therapies against emerging viruses, but which antibody features and in vitro assays best forecast protection are unclear. Our international consortium ...Antibodies are promising post-exposure therapies against emerging viruses, but which antibody features and in vitro assays best forecast protection are unclear. Our international consortium systematically evaluated antibodies against Ebola virus (EBOV) using multidisciplinary assays. For each antibody, we evaluated epitopes recognized on the viral surface glycoprotein (GP) and secreted glycoprotein (sGP), readouts of multiple neutralization assays, fraction of virions left un-neutralized, glycan structures, phagocytic and natural killer cell functions elicited, and in vivo protection in a mouse challenge model. Neutralization and induction of multiple immune effector functions (IEFs) correlated most strongly with protection. Neutralization predominantly occurred via epitopes maintained on endosomally cleaved GP, whereas maximal IEF mapped to epitopes farthest from the viral membrane. Unexpectedly, sGP cross-reactivity did not significantly influence in vivo protection. This comprehensive dataset provides a rubric to evaluate novel antibodies and vaccine responses and a roadmap for therapeutic development for EBOV and related viruses. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.1 KB 13.1 KB | Display Display | ![]() |
Images | ![]() | 22.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 77.7 KB | Display | ![]() |
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Full document | ![]() | 76.8 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7908C ![]() 7909C ![]() 7910C ![]() 7911C ![]() 7912C ![]() 7914C ![]() 7915C ![]() 7916C ![]() 7917C ![]() 7918C ![]() 7919C ![]() 7920C ![]() 7921C ![]() 7922C ![]() 7923C ![]() 7924C ![]() 7925C ![]() 7926C ![]() 7927C ![]() 7929C ![]() 7930C ![]() 7931C ![]() 7932C ![]() 7933C ![]() 7934C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | VIC32 antibody Fab in complex with Ebola virus GP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Complex of VIC32 Fab bound to Ebola virus GP
Entire | Name: Complex of VIC32 Fab bound to Ebola virus GP |
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Components |
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-Supramolecule #1: Complex of VIC32 Fab bound to Ebola virus GP
Supramolecule | Name: Complex of VIC32 Fab bound to Ebola virus GP / type: complex / ID: 1 / Parent: 0 Details: Fab fragment generated by proteolytic cleavage of IgG antibody with papain. |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.02 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: Solution was made from 10x concentration stock. | |||||||||
Staining | Type: NEGATIVE / Material: uranyl formate Details: Stained using 2% uranyl formate on carbon-coated grids. | |||||||||
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER | |||||||||
Details | This sample was monodisperse. |
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Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 35 / Average exposure time: 0.5 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | ![]() Model: Tecnai Spirit / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: Common lines model |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 (ver. 2.1) / Number images used: 2423 |
Initial angle assignment | Type: COMMON LINE / Software - Name: EMAN2 |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: EMAN2 |