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Yorodumi- PDB-5t0d: Crystal structure of H6 hemagglutinin G225D mutant from Taiwan (2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t0d | |||||||||
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Title | Crystal structure of H6 hemagglutinin G225D mutant from Taiwan (2013) H6N1 influenza virus in complex with 3'-SLN | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Influenza virus / hemagglutinin / HA / Taiwan (2013) H6N1 / Receptor specificity | |||||||||
Function / homology | Function and homology information clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane Similarity search - Function | |||||||||
Biological species | H6N1 subtype (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.864 Å | |||||||||
Authors | Wilson, I.A. / Tzarum, N. / Zhu, X. | |||||||||
Funding support | United States, 2items
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Citation | Journal: EMBO Mol Med / Year: 2017 Title: A single mutation in Taiwanese H6N1 influenza hemagglutinin switches binding to human-type receptors. Authors: de Vries, R.P. / Tzarum, N. / Peng, W. / Thompson, A.J. / Ambepitiya Wickramasinghe, I.N. / de la Pena, A.T.T. / van Breemen, M.J. / Bouwman, K.M. / Zhu, X. / McBride, R. / Yu, W. / Sanders, ...Authors: de Vries, R.P. / Tzarum, N. / Peng, W. / Thompson, A.J. / Ambepitiya Wickramasinghe, I.N. / de la Pena, A.T.T. / van Breemen, M.J. / Bouwman, K.M. / Zhu, X. / McBride, R. / Yu, W. / Sanders, R.W. / Verheije, M.H. / Wilson, I.A. / Paulson, J.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t0d.cif.gz | 304.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t0d.ent.gz | 245.6 KB | Display | PDB format |
PDBx/mmJSON format | 5t0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/5t0d ftp://data.pdbj.org/pub/pdb/validation_reports/t0/5t0d | HTTPS FTP |
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-Related structure data
Related structure data | 5t08SC 5t0bC 5t0eC 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
#1: Protein | Mass: 37389.191 Da / Num. of mol.: 3 / Mutation: G225D Source method: isolated from a genetically manipulated source Source: (gene. exp.) H6N1 subtype (virus) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X268 #2: Protein | Mass: 20631.859 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) H6N1 subtype (virus) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X267 #3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine | #4: Sugar | #5: 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: 2.79 Å3/Da / Density % sol: 55.94 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10mM NiCl2, 0.1M Tris pH 8.5, 20% (w/v) MPEG 2000 and 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→50 Å / Num. obs: 43053 / % possible obs: 97.5 % / Redundancy: 3.7 % / Rsym value: 0.08 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.86→2.91 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T08 Resolution: 2.864→49.378 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.864→49.378 Å
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Refine LS restraints |
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LS refinement shell |
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