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Yorodumi- PDB-8phi: Crystal structure of prefusion-stabilized RSV F Variant DS-Cav1 i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8phi | ||||||
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Title | Crystal structure of prefusion-stabilized RSV F Variant DS-Cav1 in complex with Lonafarnib | ||||||
Components | Fusion glycoprotein F0 | ||||||
Keywords | VIRAL PROTEIN / RSV F Glycoprotein / inhibitor | ||||||
Function / homology | Function and homology information positive regulation of syncytium formation by virus / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Human respiratory syncytial virus A2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.289 Å | ||||||
Authors | Rajak, M. / Krey, T. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Drug repurposing screen identifies lonafarnib as respiratory syncytial virus fusion protein inhibitor. Authors: Sake, S.M. / Zhang, X. / Rajak, M.K. / Urbanek-Quaing, M. / Carpentier, A. / Gunesch, A.P. / Grethe, C. / Matthaei, A. / Ruckert, J. / Galloux, M. / Larcher, T. / Le Goffic, R. / Hontonnou, ...Authors: Sake, S.M. / Zhang, X. / Rajak, M.K. / Urbanek-Quaing, M. / Carpentier, A. / Gunesch, A.P. / Grethe, C. / Matthaei, A. / Ruckert, J. / Galloux, M. / Larcher, T. / Le Goffic, R. / Hontonnou, F. / Chatterjee, A.K. / Johnson, K. / Morwood, K. / Rox, K. / Elgaher, W.A.M. / Huang, J. / Wetzke, M. / Hansen, G. / Fischer, N. / Eleouet, J.F. / Rameix-Welti, M.A. / Hirsch, A.K.H. / Herold, E. / Empting, M. / Lauber, C. / Schulz, T.F. / Krey, T. / Haid, S. / Pietschmann, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8phi.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8phi.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 8phi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/8phi ftp://data.pdbj.org/pub/pdb/validation_reports/ph/8phi | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules F
#1: Protein | Mass: 61581.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human respiratory syncytial virus A2 / Strain: strain A2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: W8RJF9 |
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-Non-polymers , 5 types, 182 molecules
#2: Chemical | ChemComp-336 / | ||||
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#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.12 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 6000-20%, CaCl2-400mM, & TrisHCl pH-8 100mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91983 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91983 Å / Relative weight: 1 |
Reflection | Resolution: 2.289→50 Å / Num. obs: 51465 / % possible obs: 99.9 % / Redundancy: 26.1 % / CC1/2: 0.997 / Rrim(I) all: 0.243 / Net I/σ(I): 10.54 |
Reflection shell | Resolution: 2.289→2.35 Å / Mean I/σ(I) obs: 1.66 / Num. unique obs: 3770 / CC1/2: 0.882 / Rrim(I) all: 1.755 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.289→26.21 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.891 / SU R Cruickshank DPI: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.257 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.198
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Displacement parameters | Biso mean: 65.03 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.289→26.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.29→2.31 Å / Total num. of bins used: 51
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