+Open data
-Basic information
Entry | Database: PDB / ID: 6qd8 | |||||||||
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Title | EM structure of a EBOV-GP bound to 4M0368 neutralizing antibody | |||||||||
Components |
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Keywords | VIRAL PROTEIN / Antibody / immune response / viral infection / EBOV | |||||||||
Function / homology | Function and homology information host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell plasma membrane / virion membrane / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Ebola virus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Diskin, R. / Cohen-Dvashi, H. | |||||||||
Citation | Journal: Nat Med / Year: 2019 Title: Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV. Authors: Stefanie A Ehrhardt / Matthias Zehner / Verena Krähling / Hadas Cohen-Dvashi / Christoph Kreer / Nadav Elad / Henning Gruell / Meryem S Ercanoglu / Philipp Schommers / Lutz Gieselmann / ...Authors: Stefanie A Ehrhardt / Matthias Zehner / Verena Krähling / Hadas Cohen-Dvashi / Christoph Kreer / Nadav Elad / Henning Gruell / Meryem S Ercanoglu / Philipp Schommers / Lutz Gieselmann / Ralf Eggeling / Christine Dahlke / Timo Wolf / Nico Pfeifer / Marylyn M Addo / Ron Diskin / Stephan Becker / Florian Klein / Abstract: Recombinant vesicular stomatitis virus-Zaire Ebola virus (rVSV-ZEBOV) is the most advanced Ebola virus vaccine candidate and is currently being used to combat the outbreak of Ebola virus disease (EVD) ...Recombinant vesicular stomatitis virus-Zaire Ebola virus (rVSV-ZEBOV) is the most advanced Ebola virus vaccine candidate and is currently being used to combat the outbreak of Ebola virus disease (EVD) in the Democratic Republic of the Congo (DRC). Here we examine the humoral immune response in a subset of human volunteers enrolled in a phase 1 rVSV-ZEBOV vaccination trial by performing comprehensive single B cell and electron microscopy structure analyses. Four studied vaccinees show polyclonal, yet reproducible and convergent B cell responses with shared sequence characteristics. EBOV-targeting antibodies cross-react with other Ebolavirus species, and detailed epitope mapping revealed overlapping target epitopes with antibodies isolated from EVD survivors. Moreover, in all vaccinees, we detected highly potent EBOV-neutralizing antibodies with activities comparable or superior to the monoclonal antibodies currently used in clinical trials. These include antibodies combining the IGHV3-15/IGLV1-40 immunoglobulin gene segments that were identified in all investigated individuals. Our findings will help to evaluate and direct current and future vaccination strategies and offer opportunities for novel EVD therapies. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6qd8.cif.gz | 331.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qd8.ent.gz | 263.6 KB | Display | PDB format |
PDBx/mmJSON format | 6qd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qd8_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6qd8_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6qd8_validation.xml.gz | 63.4 KB | Display | |
Data in CIF | 6qd8_validation.cif.gz | 95.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/6qd8 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/6qd8 | HTTPS FTP |
-Related structure data
Related structure data | 4521MC 4520C 6qd7C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 6 molecules ACEBFD
#2: Protein | Mass: 34887.578 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ebola virus / Gene: GP / Cell (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q05320 #3: Protein | Mass: 18989.391 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ebola virus / Gene: GP / Cell (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q05320 |
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-Antibody , 2 types, 6 molecules ZYLHWQ
#1: Antibody | Mass: 23411.900 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293 / Production host: Homo sapiens (human) #4: Antibody | Mass: 23091.916 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293 / Production host: Homo sapiens (human) |
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-Sugars , 2 types, 6 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.6 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 96000 X / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 27 sec. / Electron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_3297: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 123880 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123880 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5JQ3 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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