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Yorodumi- PDB-8a1e: Rabies virus glycoprotein in complex with Fab fragments of 17C7 a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a1e | ||||||||||||||||||||||||
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Title | Rabies virus glycoprotein in complex with Fab fragments of 17C7 and 1112-1 neutralizing antibodies | ||||||||||||||||||||||||
Components |
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Keywords | VIRAL PROTEIN / Viral Glycoprotein / Antibody / Complex | ||||||||||||||||||||||||
Function / homology | Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / membrane => GO:0016020 / viral envelope / virion membrane / Glycoprotein Function and homology information | ||||||||||||||||||||||||
Biological species | Rabies virus strain Pasteur vaccin Homo sapiens (human) Mus musculus (house mouse) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å | ||||||||||||||||||||||||
Authors | Ng, W.M. / Fedosyuk, S. / English, S. / Augusto, G. / Berg, A. / Thorley, L. / Haselon, A.S. / Segireddy, R.R. / Bowden, T.A. / Douglas, A.D. | ||||||||||||||||||||||||
Funding support | United Kingdom, European Union, 7items
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Citation | Journal: Cell Host Microbe / Year: 2022 Title: Structure of trimeric pre-fusion rabies virus glycoprotein in complex with two protective antibodies. Authors: Weng M Ng / Sofiya Fedosyuk / Solomon English / Gilles Augusto / Adam Berg / Luke Thorley / Anna-Sophie Haselon / Rameswara R Segireddy / Thomas A Bowden / Alexander D Douglas / Abstract: Rabies virus (RABV) causes lethal encephalitis and is responsible for approximately 60,000 deaths per year. As the sole virion-surface protein, the rabies virus glycoprotein (RABV-G) mediates host- ...Rabies virus (RABV) causes lethal encephalitis and is responsible for approximately 60,000 deaths per year. As the sole virion-surface protein, the rabies virus glycoprotein (RABV-G) mediates host-cell entry. RABV-G's pre-fusion trimeric conformation displays epitopes bound by protective neutralizing antibodies that can be induced by vaccination or passively administered for post-exposure prophylaxis. We report a 2.8-Å structure of a RABV-G trimer in the pre-fusion conformation, in complex with two neutralizing and protective monoclonal antibodies, 17C7 and 1112-1, that recognize distinct epitopes. One of these antibodies is a licensed prophylactic (17C7, Rabishield), which we show locks the protein in pre-fusion conformation. Targeted mutations can similarly stabilize RABV-G in the pre-fusion conformation, a key step toward structure-guided vaccine design. These data reveal the higher-order architecture of a key therapeutic target and the structural basis of neutralization by antibodies binding two key antigenic sites, and this will facilitate the development of improved vaccines and prophylactic antibodies. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a1e.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a1e.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 8a1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a1e_validation.pdf.gz | 967.3 KB | Display | wwPDB validaton report |
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Full document | 8a1e_full_validation.pdf.gz | 973.7 KB | Display | |
Data in XML | 8a1e_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 8a1e_validation.cif.gz | 56.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/8a1e ftp://data.pdbj.org/pub/pdb/validation_reports/a1/8a1e | HTTPS FTP |
-Related structure data
Related structure data | 15073MC 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
#1: Protein | Mass: 56494.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rabies virus strain Pasteur vaccin / Strain: Pasteur vaccins / PV / Production host: Homo sapiens (human) / References: UniProt: P08667 |
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#2: Antibody | Mass: 13227.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 11754.044 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#4: Antibody | Mass: 11668.073 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) |
#5: Antibody | Mass: 13426.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) |
-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: Rabies virus glycoprotein (chain A) in complex with Fab 1112-1 (chains B and C) and Fab 17C7 (chains D and E) Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.33 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Rabies lyssavirus | |||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Purified sample was concentrated and mixed with 0.07% n-octyl-beta-d-glucoside to final concentrations of 1 mg/mL. | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K Details: Blot for 3.5 seconds at -15 N blot force before plunging. |
-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: 81000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3.7 sec. / Electron dose: 44.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12884 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3112037 Details: Particles were automatically picked using circular blobs with a diameter of 80-150 Angstrom on cryoSPARC. | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 458014 / Details: cryoSPARC non-uniform refinement was used. / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 108 / Protocol: RIGID BODY FIT / Space: REAL Details: Model building was performed with Coot and refined with Phenix. | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.69 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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