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Yorodumi- PDB-7u9g: Rabies virus glycoprotein pre-fusion trimer in complex with neutr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7u9g | ||||||||||||
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Title | Rabies virus glycoprotein pre-fusion trimer in complex with neutralizing antibody RVA122 | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Rabies virus glycoprotein / antibodies / viral fusion protein / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||||||||
Function / homology | Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / membrane => GO:0016020 / viral envelope / virion membrane / Glycoprotein Function and homology information | ||||||||||||
Biological species | Rabies virus Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å | ||||||||||||
Authors | Callaway, H.M. / Zyla, D. / Larrous, F. / Dias de Melo, G. / Hastie, K.M. / Avalos, R.D. / Agarwal, A. / Bouhry, H. / Corti, D. / Saphire, E.O. | ||||||||||||
Funding support | United States, Switzerland, 3items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structure of the rabies virus glycoprotein trimer bound to a prefusion-specific neutralizing antibody. Authors: Heather M Callaway / Dawid Zyla / Florence Larrous / Guilherme Dias de Melo / Kathryn M Hastie / Ruben Diaz Avalos / Alyssa Agarwal / Davide Corti / Hervé Bourhy / Erica Ollmann Saphire / Abstract: Rabies infection is nearly 100% lethal if untreated and kills more than 50,000 people annually, many of them children. Existing rabies vaccines target the rabies virus glycoprotein (RABV-G) but ...Rabies infection is nearly 100% lethal if untreated and kills more than 50,000 people annually, many of them children. Existing rabies vaccines target the rabies virus glycoprotein (RABV-G) but generate short-lived immune responses, likely because the protein is heterogeneous under physiological conditions. Here, we report the 3.39 Å cryo-electron microscopy structure of trimeric, prefusion RABV-G complexed with RVA122, a potently neutralizing human antibody. RVA122 binds to a quaternary epitope at the top of RABV-G, bridging domains and stabilizing RABV-G protomers in a prefusion state. RABV-G trimerization involves side-to-side interactions between the central α helix and adjacent loops, rather than contacts between central helices, and interactions among the fusion loops at the glycoprotein base. These results provide a basis from which to develop improved rabies vaccines based on RABV-G stabilized in the prefusion conformation. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u9g.cif.gz | 330.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u9g.ent.gz | 268.6 KB | Display | PDB format |
PDBx/mmJSON format | 7u9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u9g_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7u9g_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7u9g_validation.xml.gz | 56.8 KB | Display | |
Data in CIF | 7u9g_validation.cif.gz | 85.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/7u9g ftp://data.pdbj.org/pub/pdb/validation_reports/u9/7u9g | HTTPS FTP |
-Related structure data
Related structure data | 26397MC 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: 49273.547 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rabies virus / Strain: Pasteur vaccins / PV / Cell line (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: P08667 #2: Antibody | Mass: 23449.830 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) #3: Antibody | Mass: 28196.096 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: Sugar | ChemComp-NAG / 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: Rabies virus glycoprotein pre-fusion trimer in complex with neutralizing antibody RVA122 Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 / Details: PBS pH 7.4 with 0.09mM LMNG | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid type: C-flat-2/1 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 277 K |
-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 defocus max: 3000 nm / Nominal defocus min: 500 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.2/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package | |||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 223093 / Symmetry type: POINT |