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Yorodumi- EMDB-6152: Structures of Protective Antibodies Reveal Sites of Vulnerability... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6152 | |||||||||
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Title | Structures of Protective Antibodies Reveal Sites of Vulnerability on Ebola Virus | |||||||||
Map data | Reconstruction of Ebola virus glycoprotein bound to Fab fragments of c13C6 and c4G7 | |||||||||
Sample |
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Keywords | Ebola / Antibody cocktails / mAbs / ZMAb / ZMapp / MB-003 | |||||||||
Biological species | Ebola virus sp. / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 24.0 Å | |||||||||
Authors | Murin CD / Fusco ML / Bornholdt ZA / Qiu X / Olinger GG / Zeitlin L / Kobinger GP / Ward AB / Saphire EO | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2014 Title: Structures of protective antibodies reveal sites of vulnerability on Ebola virus. Authors: Charles D Murin / Marnie L Fusco / Zachary A Bornholdt / Xiangguo Qiu / Gene G Olinger / Larry Zeitlin / Gary P Kobinger / Andrew B Ward / Erica Ollmann Saphire / Abstract: Ebola virus (EBOV) and related filoviruses cause severe hemorrhagic fever, with up to 90% lethality, and no treatments are approved for human use. Multiple recent outbreaks of EBOV and the likelihood ...Ebola virus (EBOV) and related filoviruses cause severe hemorrhagic fever, with up to 90% lethality, and no treatments are approved for human use. Multiple recent outbreaks of EBOV and the likelihood of future human exposure highlight the need for pre- and postexposure treatments. Monoclonal antibody (mAb) cocktails are particularly attractive candidates due to their proven postexposure efficacy in nonhuman primate models of EBOV infection. Two candidate cocktails, MB-003 and ZMAb, have been extensively evaluated in both in vitro and in vivo studies. Recently, these two therapeutics have been combined into a new cocktail named ZMapp, which showed increased efficacy and has been given compassionately to some human patients. Epitope information and mechanism of action are currently unknown for most of the component mAbs. Here we provide single-particle EM reconstructions of every mAb in the ZMapp cocktail, as well as additional antibodies from MB-003 and ZMAb. Our results illuminate key and recurring sites of vulnerability on the EBOV glycoprotein and provide a structural rationale for the efficacy of ZMapp. Interestingly, two of its components recognize overlapping epitopes and compete with each other for binding. Going forward, this work now provides a basis for strategic selection of next-generation antibody cocktails against Ebola and related viruses and a model for predicting the impact of ZMapp on potential escape mutations in ongoing or future Ebola outbreaks. | |||||||||
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_6152.map.gz | 1.6 MB | EMDB map data format | |
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Header (meta data) | emd-6152-v30.xml emd-6152.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_6152.jpg | 143.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6152 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6152 | HTTPS FTP |
-Validation report
Summary document | emd_6152_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_6152_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_6152_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6152 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6152 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6152.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Ebola virus glycoprotein bound to Fab fragments of c13C6 and c4G7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 c13C6 and c4G7 chimerized human monoclonal IgG1 a...
Entire | Name: Fab fragment of c13C6 and c4G7 chimerized human monoclonal IgG1 antibody bound to Ebola virus glycoprotein |
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Components |
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-Supramolecule #1000: Fab fragment of c13C6 and c4G7 chimerized human monoclonal IgG1 a...
Supramolecule | Name: Fab fragment of c13C6 and c4G7 chimerized human monoclonal IgG1 antibody bound to Ebola virus glycoprotein type: sample / ID: 1000 Oligomeric state: Six Fab fragments bound to a single, trimeric GP (two Fabs per protomer) Number unique components: 3 |
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Molecular weight | Theoretical: 750 KDa |
-Macromolecule #1: Ebola virus glycoprotein
Macromolecule | Name: Ebola virus glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: EBOV GP / Number of copies: 1 / Oligomeric state: trimer / Recombinant expression: Yes |
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Source (natural) | Organism: Ebola virus sp. |
Molecular weight | Theoretical: 450 KDa |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) / Recombinant cell: Schneider 2 (S2) / Recombinant plasmid: pMT-puro |
-Macromolecule #2: chimerized human IgG1 antigen binding fragment c13C6
Macromolecule | Name: chimerized human IgG1 antigen binding fragment c13C6 / type: protein_or_peptide / ID: 2 / Name.synonym: c13C6 Fab / Number of copies: 3 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
-Macromolecule #3: chimerized human IgG1 antigen binding fragment c4G7
Macromolecule | Name: chimerized human IgG1 antigen binding fragment c4G7 / type: protein_or_peptide / ID: 3 / Name.synonym: c4G7 Fab / Number of copies: 3 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
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 |
Staining | Type: NEGATIVE Details: To prepare negative stain grids, a 4 uL aliquot of each complex, which had been diluted to a concentration of ~0.03 ug/mL with TBS buffer, was placed for 15 seconds onto carbon-coated 400 Cu ...Details: To prepare negative stain grids, a 4 uL aliquot of each complex, which had been diluted to a concentration of ~0.03 ug/mL with TBS buffer, was placed for 15 seconds onto carbon-coated 400 Cu mesh grids that had been plasma cleaned for 20 s (Gatan), blotted off on the edge of the grid, then immediately stained for 30 s with 4 uL of 2% uranyl formate. The stain was blotted off on the edge of the grid and the grid was allowed to dry. |
Grid | Details: 400 Cu mesh |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Feb 5, 2014 |
Image recording | Category: CCD / Film or detector model: OTHER / Number real images: 65 |
Electron beam | Acceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: OTHER / Software - Name: EMAN2, XMipp, IMAGIC / Number images used: 10210 |
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