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Yorodumi- PDB-5ea5: Crystal Structure of Inhibitor TMC-353121 in Complex with Prefusi... -
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-Basic information
Entry | Database: PDB / ID: 5ea5 | ||||||
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Title | Crystal Structure of Inhibitor TMC-353121 in Complex with Prefusion RSV F Glycoprotein | ||||||
Components | Fusion glycoprotein F0 | ||||||
Keywords | CELL INVASION/INHIBITOR / Class I viral fusion protein / fusion / respiratory syncytial virus / prefusion / viral protein / fusion inhibitor / CELL INVASION-INHIBITOR complex | ||||||
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 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Human respiratory syncytial virus A | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | ||||||
Authors | Battles, M.B. / McLellan, J.S. / Arnoult, E. / Roymans, D. / Langedijk, J.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Molecular mechanism of respiratory syncytial virus fusion inhibitors. Authors: Battles, M.B. / Langedijk, J.P. / Furmanova-Hollenstein, P. / Chaiwatpongsakorn, S. / Costello, H.M. / Kwanten, L. / Vranckx, L. / Vink, P. / Jaensch, S. / Jonckers, T.H. / Koul, A. / ...Authors: Battles, M.B. / Langedijk, J.P. / Furmanova-Hollenstein, P. / Chaiwatpongsakorn, S. / Costello, H.M. / Kwanten, L. / Vranckx, L. / Vink, P. / Jaensch, S. / Jonckers, T.H. / Koul, A. / Arnoult, E. / Peeples, M.E. / Roymans, D. / McLellan, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ea5.cif.gz | 190.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ea5.ent.gz | 148.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ea5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/5ea5 ftp://data.pdbj.org/pub/pdb/validation_reports/ea/5ea5 | HTTPS FTP |
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-Related structure data
Related structure data | 5ea3C 5ea4C 5ea6C 5ea7C 5ea8C 4mmsS C: citing same article (ref.) 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
#1: Protein | Mass: 63218.344 Da / Num. of mol.: 1 / Fragment: RSV F ectodomain (UNP residues 1-513) / Mutation: S190F, V207L, S155C, S290C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human respiratory syncytial virus A (strain A2) Strain: A2 / Plasmid: p(alpha)H / Cell line (production host): HEK293 FreeStyle / Production host: Homo sapiens (human) / References: UniProt: P03420 |
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#2: Chemical | ChemComp-NHE / |
#3: Chemical | ChemComp-TM3 / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-TAR / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 1.54 M potassium/sodium tartrate, 0.2 M lithium sulfate, 0.1 M CHES, pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2014 | |||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 3.05→49.03 Å / Num. obs: 16585 / % possible obs: 100 % / Redundancy: 25.2 % / Biso Wilson estimate: 72.34 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.317 / Rpim(I) all: 0.064 / Net I/σ(I): 11.9 / Num. measured all: 418216 / Scaling rejects: 2404 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4MMS Resolution: 3.05→49.03 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 230.02 Å2 / Biso mean: 82.6233 Å2 / Biso min: 31.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.05→49.03 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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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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