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- PDB-3ubn: Influenza hemagglutinin from the 2009 pandemic in complex with li... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ubn | |||||||||
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Title | Influenza hemagglutinin from the 2009 pandemic in complex with ligand 6SLN | |||||||||
![]() | (Hemagglutinin ...) x 2 | |||||||||
![]() | VIRAL PROTEIN/IMMUNE SYSTEM / viral envelope protein / hemagglutinin / viral fusion protein / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Xu, R. / Wilson, I.A. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 591 KB | Display | ![]() |
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PDB format | ![]() | 489.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ubeC ![]() 3ubjC ![]() 3ubqC ![]() 3lzgS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() |
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-Sugars , 4 types, 16 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine #4: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #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 / |
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-Non-polymers , 1 types, 485 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: 2.33 Å3/Da / Density % sol: 47.11 % |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 2.1 % / Av σ(I) over netI: 9.23 / Number: 207943 / Rmerge(I) obs: 0.087 / Χ2: 1.03 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 99231 / % possible obs: 94.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.5→50 Å / Num. obs: 99231 / % possible obs: 94.6 % / Redundancy: 2.1 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.033 / Net I/σ(I): 7.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 41.02 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3LZG Resolution: 2.5079→49.682 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 1.97 / Phase error: 29.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.775 Å2 / ksol: 0.343 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.93 Å2 / Biso mean: 48.8788 Å2 / Biso min: 22.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5079→49.682 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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