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Yorodumi- PDB-7uj3: Crystal structure of Human respiratory syncytial virus F variant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uj3 | ||||||
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Title | Crystal structure of Human respiratory syncytial virus F variant (construct pXCS847A) | ||||||
Components |
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Keywords | VIRUS / RSV / RSVF / pre-fusion | ||||||
Function / homology | Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0 Function and homology information | ||||||
Biological species | Respiratory syncytial virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Han, S. / Ammirati, M. | ||||||
Funding support | 1items
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Citation | Journal: Sci Transl Med / Year: 2023 Title: Rational design of a highly immunogenic prefusion-stabilized F glycoprotein antigen for a respiratory syncytial virus vaccine. Authors: Ye Che / Alexey V Gribenko / Xi Song / Luke D Handke / Kari S Efferen / Kristin Tompkins / Srinivas Kodali / Lorna Nunez / A Krishna Prasad / Lynn M Phelan / Mark Ammirati / Xiaodi Yu / ...Authors: Ye Che / Alexey V Gribenko / Xi Song / Luke D Handke / Kari S Efferen / Kristin Tompkins / Srinivas Kodali / Lorna Nunez / A Krishna Prasad / Lynn M Phelan / Mark Ammirati / Xiaodi Yu / Joshua A Lees / Wei Chen / Lyndsey Martinez / Vidia Roopchand / Seungil Han / Xiayang Qiu / John P DeVincenzo / Kathrin U Jansen / Philip R Dormitzer / Kena A Swanson / Abstract: Respiratory syncytial virus (RSV) is the leading, global cause of serious respiratory disease in infants and is an important cause of respiratory illness in older adults. No RSV vaccine is currently ...Respiratory syncytial virus (RSV) is the leading, global cause of serious respiratory disease in infants and is an important cause of respiratory illness in older adults. No RSV vaccine is currently available. The RSV fusion (F) glycoprotein is a key antigen for vaccine development, and its prefusion conformation is the target of the most potent neutralizing antibodies. Here, we describe a computational and experimental strategy for designing immunogens that enhance the conformational stability and immunogenicity of RSV prefusion F. We obtained an optimized vaccine antigen after screening nearly 400 engineered F constructs. Through in vitro and in vivo characterization studies, we identified F constructs that are more stable in the prefusion conformation and elicit ~10-fold higher serum-neutralizing titers in cotton rats than DS-Cav1. The stabilizing mutations of the lead construct (847) were introduced onto F glycoprotein backbones of strains representing the dominant circulating genotypes of the two major RSV subgroups, A and B. Immunization of cotton rats with a bivalent vaccine formulation of these antigens conferred complete protection against RSV challenge, with no evidence of disease enhancement. The resulting bivalent RSV prefusion F investigational vaccine has recently been shown to be efficacious against RSV disease in two pivotal phase 3 efficacy trials, one for passive protection of infants by immunization of pregnant women and the second for active protection of older adults by direct immunization. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uj3.cif.gz | 191.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uj3.ent.gz | 151.4 KB | Display | PDB format |
PDBx/mmJSON format | 7uj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/7uj3 ftp://data.pdbj.org/pub/pdb/validation_reports/uj/7uj3 | HTTPS FTP |
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-Related structure data
Related structure data | 7ujaC 4mmuS S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 12109.954 Da / Num. of mol.: 1 / Mutation: A100C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Respiratory syncytial virus / Production host: Mammalia (mammals) / References: UniProt: A0A7D5GVC1 | ||||
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#2: Protein | Mass: 45025.391 Da / Num. of mol.: 1 / Mutation: I145S, S187I, D483S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Respiratory syncytial virus / Production host: Mammalia (mammals) / References: UniProt: A0A7D5GVC1 | ||||
#3: Chemical | #4: Sugar | ChemComp-NAG / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Na acetate, pH 4.6, 0.2 M ammonium sulfate, and 30% poly(ethylene) glycol monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→49.08 Å / Num. obs: 11179 / % possible obs: 99.8 % / Redundancy: 38.3 % / CC1/2: 1 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 3.5→3.71 Å / Num. unique obs: 1742 / CC1/2: 0.774 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MMU Resolution: 3.5→49.08 Å / Cor.coef. Fo:Fc: 0.7211 / Cor.coef. Fo:Fc free: 0.64 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.513
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Displacement parameters | Biso max: 298.47 Å2 / Biso mean: 77.61 Å2 / Biso min: 9.48 Å2
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Refine analyze | Luzzati coordinate error obs: 0.512 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→49.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | L11: 0 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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