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- PDB-5t0d: Crystal structure of H6 hemagglutinin G225D mutant from Taiwan (2... -
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Open data
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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 | |||||||||
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![]() | IMMUNE SYSTEM / Influenza virus / hemagglutinin / HA / Taiwan (2013) H6N1 / Receptor specificity | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wilson, I.A. / Tzarum, N. / Zhu, X. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304.1 KB | Display | ![]() |
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PDB format | ![]() | 245.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 813.2 KB | Display | ![]() |
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Full document | ![]() | 835.6 KB | Display | |
Data in XML | ![]() | 54.5 KB | Display | |
Data in CIF | ![]() | 74.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5t08SC ![]() 5t0bC ![]() 5t0eC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() #2: Protein | Mass: 20631.859 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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