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Yorodumi- PDB-3ube: Influenza hemagglutinin from the 2009 pandemic in complex with li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ube | |||||||||
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Title | Influenza hemagglutinin from the 2009 pandemic in complex with ligand LSTc | |||||||||
Components | (Hemagglutinin ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / viral envelope protein / hemagglutinin / viral fusion protein / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
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 Influenza a virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Xu, R. / Wilson, I.A. | |||||||||
Citation | Journal: J.Virol. / Year: 2012 Title: Structural Characterization of the Hemagglutinin Receptor Specificity from the 2009 H1N1 Influenza Pandemic. Authors: Xu, R. / McBride, R. / Nycholat, C.M. / Paulson, J.C. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ube.cif.gz | 601.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ube.ent.gz | 497.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ube.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/3ube ftp://data.pdbj.org/pub/pdb/validation_reports/ub/3ube | HTTPS FTP |
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-Related structure data
Related structure data | 3ubjC 3ubnC 3ubqC 3lzgS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Hemagglutinin ... , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein | Mass: 36535.281 Da / Num. of mol.: 6 / Fragment: Ectodomain HA1, residues 18-344 / Mutation: G205C, R220C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: SW1 A/CALIFORNIA/04/2009 / Gene: HA, hemagglutinin / Plasmid: pFastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C3W5S1 #2: Protein | Mass: 20278.383 Da / Num. of mol.: 6 / Fragment: Ectodomain HA2, residues 345-520 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza a virus / Strain: SW1 A/CALIFORNIA/04/2009 / Gene: HA, hemagglutinin / Plasmid: pFASTbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C3W5S1 |
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-Sugars , 5 types, 14 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | #5: 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 #6: Sugar | ChemComp-NAG / #7: Sugar | ChemComp-SIA / | |
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-Non-polymers , 1 types, 878 molecules
#8: 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: 2.31 Å3/Da / Density % sol: 46.65 % |
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Crystal grow | Temperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 27% PEG-MME 2000, 0.1M Tris pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2010 Details: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 153165 / % possible obs: 92.8 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LZG Resolution: 2.15→49.543 Å / SU ML: 0.33 / σ(F): 1.97 / Phase error: 28.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.825 Å2 / ksol: 0.359 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.15→49.543 Å
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Refine LS restraints |
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LS refinement shell |
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