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Yorodumi- PDB-7swd: Structure of EBOV GP lacking the mucin-like domain with 1C11 scFv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7swd | |||||||||
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Title | Structure of EBOV GP lacking the mucin-like domain with 1C11 scFv and 1C3 Fab bound | |||||||||
Components |
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Keywords | VIRAL PROTEIN/Immune System / VIRAL PROTEIN / glycoprotein / immune system / antibody / Ebola virus / VIRAL PROTEIN-Immune System complex | |||||||||
Function / homology | Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / membrane => GO:0016020 / extracellular region / Virion spike glycoprotein / Virion spike glycoprotein Function and homology information | |||||||||
Biological species | Ebola virus - Gabon Zaire ebolavirus Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å | |||||||||
Authors | Milligan, J.C. / Yu, X. / Saphire, E.O. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Cell / Year: 2022 Title: Asymmetric and non-stoichiometric glycoprotein recognition by two distinct antibodies results in broad protection against ebolaviruses. Authors: Jacob C Milligan / Carl W Davis / Xiaoying Yu / Philipp A Ilinykh / Kai Huang / Peter J Halfmann / Robert W Cross / Viktoriya Borisevich / Krystle N Agans / Joan B Geisbert / Chakravarthy ...Authors: Jacob C Milligan / Carl W Davis / Xiaoying Yu / Philipp A Ilinykh / Kai Huang / Peter J Halfmann / Robert W Cross / Viktoriya Borisevich / Krystle N Agans / Joan B Geisbert / Chakravarthy Chennareddy / Arthur J Goff / Ashley E Piper / Sean Hui / Kelly C L Shaffer / Tierra Buck / Megan L Heinrich / Luis M Branco / Ian Crozier / Michael R Holbrook / Jens H Kuhn / Yoshihiro Kawaoka / Pamela J Glass / Alexander Bukreyev / Thomas W Geisbert / Gabriella Worwa / Rafi Ahmed / Erica Ollmann Saphire / Abstract: Several ebolaviruses cause outbreaks of severe disease. Vaccines and monoclonal antibody cocktails are available to treat Ebola virus (EBOV) infections, but not Sudan virus (SUDV) or other ...Several ebolaviruses cause outbreaks of severe disease. Vaccines and monoclonal antibody cocktails are available to treat Ebola virus (EBOV) infections, but not Sudan virus (SUDV) or other ebolaviruses. Current cocktails contain antibodies that cross-react with the secreted soluble glycoprotein (sGP) that absorbs virus-neutralizing antibodies. By sorting memory B cells from EBOV infection survivors, we isolated two broadly reactive anti-GP monoclonal antibodies, 1C3 and 1C11, that potently neutralize, protect rodents from disease, and lack sGP cross-reactivity. Both antibodies recognize quaternary epitopes in trimeric ebolavirus GP. 1C11 bridges adjacent protomers via the fusion loop. 1C3 has a tripartite epitope in the center of the trimer apex. One 1C3 antigen-binding fragment anchors simultaneously to the three receptor-binding sites in the GP trimer, and separate 1C3 paratope regions interact differently with identical residues on the three protomers. A cocktail of both antibodies completely protected nonhuman primates from EBOV and SUDV infections, indicating their potential clinical value. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7swd.cif.gz | 290.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7swd.ent.gz | 236.7 KB | Display | PDB format |
PDBx/mmJSON format | 7swd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/7swd ftp://data.pdbj.org/pub/pdb/validation_reports/sw/7swd | HTTPS FTP |
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-Related structure data
Related structure data | 25471MC 7n6pC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Virion spike glycoprotein ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 31297.158 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ebola virus - Gabon (1994-1997) / Strain: Mayinga-76 / Gene: GP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A089X075 #2: Protein | Mass: 10756.211 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zaire ebolavirus / Gene: GP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A7S6GAH2 |
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-Antibody , 3 types, 5 molecules GHIJK
#3: Antibody | Mass: 26783.773 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly) #4: Antibody | | Mass: 13308.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #5: Antibody | | Mass: 12624.050 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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-Sugars , 1 types, 3 molecules
#6: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Details
Has ligand of interest | N |
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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
Component | Name: Complex of EBOV GP lacking the mucin-like-domain with 1C11 scFv and 1C3 Fab Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 0.3 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Drosophila (fruit flies) |
Buffer solution | pH: 7.4 |
Buffer component | Name: TBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Image recording | Average exposure time: 54.95 sec. / Electron dose: 34.97 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75948 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||
Refine LS restraints |
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