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Yorodumi- PDB-6eal: CRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eal | |||||||||
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Title | CRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN INHIBITOR ESCAPE VARIANT D486N STABILIZED IN THE PREFUSION STATE | |||||||||
Components | Fusion glycoprotein F0 | |||||||||
Keywords | VIRAL PROTEIN / CLASS I VIRAL FUSION PROTEIN / FUSION / RESPIRATORY SYNCYTIAL VIRUS / PREFUSION / FUSION 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 / 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 / plasma membrane Similarity search - Function | |||||||||
Biological species | Human respiratory syncytial virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.751 Å | |||||||||
Authors | Battles, M.B. / McLellan, J.S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Structural Basis for Respiratory Syncytial Virus Fusion Inhibitor Resistance Authors: Battles, M.B. / 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 | 6eal.cif.gz | 189.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eal.ent.gz | 147.8 KB | Display | PDB format |
PDBx/mmJSON format | 6eal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/6eal ftp://data.pdbj.org/pub/pdb/validation_reports/ea/6eal | HTTPS FTP |
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-Related structure data
Related structure data | 6eadC 6eaeC 6eafC 6eagC 6eahC 6eaiC 6eajC 6eakC 6eamC 6eanC 5ea3S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 63217.359 Da / Num. of mol.: 1 / Fragment: RSV F ectodomain / Mutation: S155C, S290C, S190F, V207L, D486N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human respiratory syncytial virus / Plasmid: P(ALPHA)H / Production host: Homo sapiens (human) / Strain (production host): HEK293 FREESTYLE / References: UniProt: W8RJF9, UniProt: P03420*PLUS | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NHE / | #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: 3.27 Å3/Da / Density % sol: 62.41 % / Mosaicity: 0.52 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 1.56M K/Na tartrate, 0.2M LiSO4, 0.1M CHES pH 9.5, 2% DMSO |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 18, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→47.32 Å / Num. obs: 22649 / % possible obs: 99.9 % / Redundancy: 13.7 % / Biso Wilson estimate: 55.63 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.067 / Rrim(I) all: 0.253 / Net I/σ(I): 10.6 / Num. measured all: 309225 / Scaling rejects: 65 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 11.9 % / Rmerge(I) obs: 2.121 / Num. measured all: 37903 / Num. unique obs: 3195 / CC1/2: 0.508 / Rpim(I) all: 0.621 / Rrim(I) all: 2.215 / Net I/σ(I) obs: 1.6 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EA3 Resolution: 2.751→47.316 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.07 / 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: 197.34 Å2 / Biso mean: 67.8913 Å2 / Biso min: 16.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.751→47.316 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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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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