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Yorodumi- PDB-6eak: CRYSTAL STRUCTURE OF FUSION INHIBITOR JNJ-2408068 IN COMPLEX WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eak | |||||||||
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Title | CRYSTAL STRUCTURE OF FUSION INHIBITOR JNJ-2408068 IN COMPLEX WITH HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN ESCAPE VARIANT T400A 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: 2.6 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 | 6eak.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eak.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 6eak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/6eak ftp://data.pdbj.org/pub/pdb/validation_reports/ea/6eak | HTTPS FTP |
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-Related structure data
Related structure data | 6eadC 6eaeC 6eafC 6eagC 6eahC 6eaiC 6eajC 6ealC 6eamC 6eanC 5ea4S 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
-Protein , 1 types, 1 molecules F
#1: Protein | Mass: 63188.320 Da / Num. of mol.: 1 / Fragment: RSV F ectodomain / Mutation: S155C, S290C, S190F, V207L, T400A 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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-Non-polymers , 5 types, 64 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NHE / | #4: Chemical | ChemComp-NI / | #5: Chemical | ChemComp-5NK / | #6: Water | ChemComp-HOH / | |
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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: 3.15 Å3/Da / Density % sol: 60.98 % / Mosaicity: 0.66 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 1.48M K/Na tartrate, 0.2M LiSO4, 0.1M CHES pH 9.5 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→59.56 Å / Num. obs: 25761 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 55.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.035 / Rrim(I) all: 0.135 / Net I/σ(I): 15.5 / Num. measured all: 376488 / Scaling rejects: 9 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 15.6 % / Rmerge(I) obs: 1.267 / Num. unique obs: 3084 / CC1/2: 0.795 / Rpim(I) all: 0.33 / Rrim(I) all: 1.31 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EA4 Resolution: 2.6→59.556 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 155.93 Å2 / Biso mean: 62.1724 Å2 / Biso min: 23.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→59.556 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %
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