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Yorodumi- PDB-4we8: The crystal structure of hemagglutinin of influenza virus A/Victo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4we8 | ||||||||||||
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Title | The crystal structure of hemagglutinin of influenza virus A/Victoria/361/2011 | ||||||||||||
Components | Hemagglutinin | ||||||||||||
Keywords | VIRAL PROTEIN / Hemagglutinin / H3N2 / influenza virus | ||||||||||||
Function / homology | Function and homology information viral budding from plasma membrane / 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 / virion membrane Similarity search - Function | ||||||||||||
Biological species | Influenza A virus | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||||||||
Authors | Yang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J. | ||||||||||||
Citation | Journal: Virology / Year: 2015 Title: Structure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins. Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4we8.cif.gz | 123.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4we8.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 4we8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/4we8 ftp://data.pdbj.org/pub/pdb/validation_reports/we/4we8 | HTTPS FTP |
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-Related structure data
Related structure data | 4we4C 4we5C 4we6C 4we7C 4we9C 4weaC 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: 57840.719 Da / Num. of mol.: 1 / Fragment: unp residues 17-519 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Singapore/H2011.447/2011(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R9U684 | ||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||
#3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.12 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 10.5 / Details: 0.1M CAPS:NaOH, 30% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 43789 / Num. obs: 43789 / % possible obs: 98.5 % / Redundancy: 5.1 % / Net I/σ(I): 37.1 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→34.156 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.29 / 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: 2.1→34.156 Å
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Refine LS restraints |
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LS refinement shell |
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