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Yorodumi- PDB-6q0s: Crystal Structure of RSV strain B18537 Prefusion-stabilized glyco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q0s | ||||||
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Title | Crystal Structure of RSV strain B18537 Prefusion-stabilized glycoprotein F Variant DS-Cav1 | ||||||
Components | Fusion glycoprotein F0 | ||||||
Keywords | IMMUNE SYSTEM / Respiratory syncytial virus / structure-based vaccine design | ||||||
Function / homology | Function and homology information positive regulation of syncytium formation by virus / host cell Golgi membrane / membrane => GO:0016020 / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane Similarity search - Function | ||||||
Biological species | Human respiratory syncytial virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Joyce, M.G. / Bao, A. / Kwong, P.D. | ||||||
Citation | Journal: Pathog Immun / Year: 2019 Title: Crystal Structure and Immunogenicity of the DS-Cav1-Stabilized Fusion Glycoprotein From Respiratory Syncytial Virus Subtype B. Authors: Joyce, M.G. / Bao, A. / Chen, M. / Georgiev, I.S. / Ou, L. / Bylund, T. / Druz, A. / Kong, W.P. / Peng, D. / Rundlet, E.J. / Van Galen, J.G. / Wang, S. / Yang, Y. / Zhang, B. / Chuang, G.Y. ...Authors: Joyce, M.G. / Bao, A. / Chen, M. / Georgiev, I.S. / Ou, L. / Bylund, T. / Druz, A. / Kong, W.P. / Peng, D. / Rundlet, E.J. / Van Galen, J.G. / Wang, S. / Yang, Y. / Zhang, B. / Chuang, G.Y. / McLellan, J.S. / Graham, B.S. / Mascola, J.R. / Kwong, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q0s.cif.gz | 276.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q0s.ent.gz | 227.9 KB | Display | PDB format |
PDBx/mmJSON format | 6q0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/6q0s ftp://data.pdbj.org/pub/pdb/validation_reports/q0/6q0s | HTTPS FTP |
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-Related structure data
Related structure data | 4mmuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 61307.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human respiratory syncytial virus (subgroup B / strain 18537) Strain: 18537 / Production host: Homo sapiens (human) / References: UniProt: P13843 | ||||||
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#2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 3.22 Å3/Da / Density % sol: 61.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.2 M ammonium sulfate, 0.1 M lithium sulfate, 0.1 M sodium acetate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. obs: 57616 / % possible obs: 95.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.96 |
Reflection shell | Resolution: 1.94→2.01 Å / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 3616 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MMU Resolution: 1.94→34.27 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.49 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 182.42 Å2 / Biso mean: 53.63 Å2 / Biso min: 0.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→34.27 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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