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Yorodumi- PDB-6vtw: De novo protein design enables the precise induction of RSV-neutr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vtw | |||||||||
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Title | De novo protein design enables the precise induction of RSV-neutralizing antibodies | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / de novo designed / immunogens / antibodies / in vivo | |||||||||
Biological species | Mus musculus (house mouse) Human respiratory syncytial virus A2 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Jardetzky, T. / Correia, B. | |||||||||
Funding support | Switzerland, European Union, 2items
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Citation | Journal: Science / Year: 2020 Title: De novo protein design enables the precise induction of RSV-neutralizing antibodies. Authors: Sesterhenn, F. / Yang, C. / Bonet, J. / Cramer, J.T. / Wen, X. / Wang, Y. / Chiang, C.I. / Abriata, L.A. / Kucharska, I. / Castoro, G. / Vollers, S.S. / Galloux, M. / Dheilly, E. / Rosset, S. ...Authors: Sesterhenn, F. / Yang, C. / Bonet, J. / Cramer, J.T. / Wen, X. / Wang, Y. / Chiang, C.I. / Abriata, L.A. / Kucharska, I. / Castoro, G. / Vollers, S.S. / Galloux, M. / Dheilly, E. / Rosset, S. / Corthesy, P. / Georgeon, S. / Villard, M. / Richard, C.A. / Descamps, D. / Delgado, T. / Oricchio, E. / Rameix-Welti, M.A. / Mas, V. / Ervin, S. / Eleouet, J.F. / Riffault, S. / Bates, J.T. / Julien, J.P. / Li, Y. / Jardetzky, T. / Krey, T. / Correia, B.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vtw.cif.gz | 284.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vtw.ent.gz | 233.8 KB | Display | PDB format |
PDBx/mmJSON format | 6vtw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vtw_validation.pdf.gz | 248.3 KB | Display | wwPDB validaton report |
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Full document | 6vtw_full_validation.pdf.gz | 248.3 KB | Display | |
Data in XML | 6vtw_validation.xml.gz | 1.2 KB | Display | |
Data in CIF | 6vtw_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/6vtw ftp://data.pdbj.org/pub/pdb/validation_reports/vt/6vtw | HTTPS FTP |
-Related structure data
Related structure data | 6s3dC 6xwiC 6xxvC 3o41S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein/peptide | Mass: 5096.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HEK293-6E cell / Source: (synth.) Human respiratory syncytial virus A2 |
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#2: Antibody | Mass: 23952.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293-F cell / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 23428.318 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HEK293-F cell / Production host: Homo sapiens (human) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.02 % / Description: cuboid |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: containing 0.2 M Magnesium acetate, 0.1 M Sodium cacodylate pH 6.5, 20 %(w/v) PEG 8000 PH range: 5.0 - 7.0 / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cold N2 stream / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→37.06 Å / Num. obs: 17472 / % possible obs: 91 % / Redundancy: 6.5 % / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.07259 / Rpim(I) all: 0.03012 / Rrim(I) all: 0.07879 / Net I/σ(I): 17.14 |
Reflection shell | Resolution: 2.6→2.693 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.8539 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 1567 / CC1/2: 0.116 / CC star: 0.456 / Rpim(I) all: 0.4332 / Rrim(I) all: 0.9625 / % possible all: 89.58 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O41 Resolution: 2.6→37.06 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→37.06 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -46.2207 Å / Origin y: -37.8662 Å / Origin z: -6.3608 Å
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Refinement TLS group | Selection details: all |