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Yorodumi- PDB-2rft: Crystal structure of influenza B virus hemagglutinin in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rft | |||||||||
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Title | Crystal structure of influenza B virus hemagglutinin in complex with LSTa receptor analog | |||||||||
Components | (Influenza B hemagglutinin ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / Influenza / receptor specificity / Envelope protein / Fusion protein / Hemagglutinin / Membrane / Transmembrane / Virion / Glycoprotein / Lipoprotein / Palmitate | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / endocytosis involved in viral entry into 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 / membrane Similarity search - Function | |||||||||
Biological species | Influenza B virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Wang, Q. / Tian, X. / Chen, X. / Ma, J. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Structural basis for receptor specificity of influenza B virus hemagglutinin. Authors: Wang, Q. / Tian, X. / Chen, X. / Ma, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rft.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rft.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 2rft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/2rft ftp://data.pdbj.org/pub/pdb/validation_reports/rf/2rft | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Influenza B hemagglutinin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 37161.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus (STRAIN B/HONG KONG/8/73) Genus: Influenzavirus BInfluenza B virus / Species: Influenza B virus / Strain: B/HongKong/8/73 / Gene: Hemagglutinin / Genus (production host): Influenzavirus B / Production host: Influenza B virus / References: UniProt: Q84097, UniProt: P03462*PLUS |
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#2: Protein | Mass: 18948.252 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus (STRAIN B/HONG KONG/8/73) Genus: Influenzavirus BInfluenza B virus / Species: Influenza B virus / Strain: B/HongKong/8/73 / Gene: Hemagglutinin / Genus (production host): Influenzavirus B / Production host: Influenza B virus / References: UniProt: Q84097, UniProt: P03462*PLUS |
-Sugars , 3 types, 8 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #4: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 1 types, 2 molecules
#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: 3.38 Å3/Da / Density % sol: 63.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM Pipes, 2.5 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2005 |
Radiation | Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→13 Å / Num. all: 21280 / Num. obs: 19145 / % possible obs: 89.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.1 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Unliganded influenza B virus hemagglutinin Resolution: 2.8→10 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.856 / SU B: 20.296 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.336 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.867 Å / Total num. of bins used: 20
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