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- PDB-4nrl: Structure of hemagglutinin with F95Y mutation of influenza virus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nrl | |||||||||
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Title | Structure of hemagglutinin with F95Y mutation of influenza virus B/Lee/40 | |||||||||
![]() | (Hemagglutinin ...) x 2 | |||||||||
![]() | VIRAL PROTEIN / HA | |||||||||
Function / homology | ![]() viral budding from plasma membrane / endocytosis involved in viral entry into host cell / host cell surface receptor binding / 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 / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ni, F. / Mbawuike, I.N. / Kondrashkina, E. / Wang, Q. | |||||||||
![]() | ![]() Title: The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Authors: Ni, F. / Nnadi Mbawuike, I. / Kondrashkina, E. / Wang, Q. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 311.8 KB | Display | ![]() |
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PDB format | ![]() | 260.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.9 MB | Display | ![]() |
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Full document | ![]() | 4.9 MB | Display | |
Data in XML | ![]() | 58.6 KB | Display | |
Data in CIF | ![]() | 79.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
-Hemagglutinin ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 37756.098 Da / Num. of mol.: 3 / Mutation: F95Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 19542.980 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 4 types, 22 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 1 types, 269 molecules ![](data/chem/img/HOH.gif)
#7: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.79 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M di-Sodium succinate 15% w/v PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.72→48.91 Å / Num. all: 61849 / Num. obs: 59313 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.72→2.87 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4 / % possible all: 87.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 2.72→47.487 Å
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Refine LS restraints |
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LS refinement shell |
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