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Yorodumi- PDB-5ea3: Crystal Structure of Inhibitor JNJ-2408068 in Complex with Prefus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ea3 | ||||||
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Title | Crystal Structure of Inhibitor JNJ-2408068 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 / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / 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 / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Human respiratory syncytial virus A | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Battles, M.B. / McLellan, J.S. / Arnoult, E. / Langedijk, J.P. / Roymans, D. | ||||||
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 | 5ea3.cif.gz | 187.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ea3.ent.gz | 147.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ea3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/5ea3 ftp://data.pdbj.org/pub/pdb/validation_reports/ea/5ea3 | HTTPS FTP |
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-Related structure data
Related structure data | 5ea4C 5ea5C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 63218.344 Da / Num. of mol.: 1 / Fragment: RSV F ectodomain (UNP residues 1-513) / Mutation: V207L, S190F, 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-SO4 / #4: Chemical | ChemComp-5NK / | #5: 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: 3.24 Å3/Da / Density % sol: 62.09 % |
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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: 5.0.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2014 | |||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.75→49.11 Å / Num. obs: 22511 / % possible obs: 100 % / Redundancy: 32.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.046 / Net I/σ(I): 17.6 / Num. measured all: 740624 / Scaling rejects: 417 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4MMS Resolution: 2.75→49.107 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.99 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 166.68 Å2 / Biso mean: 65.3997 Å2 / Biso min: 25.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→49.107 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: 8 / % reflection obs: 100 %
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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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