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Yorodumi- PDB-3ubq: Influenza hemagglutinin from the 2009 pandemic in complex with li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ubq | |||||||||
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Title | Influenza hemagglutinin from the 2009 pandemic in complex with ligand 3SLN | |||||||||
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 / molecular replacement / Resolution: 2 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 | 3ubq.cif.gz | 606.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ubq.ent.gz | 498.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ubq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ubq_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 3ubq_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 3ubq_validation.xml.gz | 114.7 KB | Display | |
Data in CIF | 3ubq_validation.cif.gz | 156.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/3ubq ftp://data.pdbj.org/pub/pdb/validation_reports/ub/3ubq | HTTPS FTP |
-Related structure data
Related structure data | 3ubeC 3ubjC 3ubnC 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 , 4 types, 18 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine | #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 1 types, 1051 molecules
#7: 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: 2.3 Å3/Da / Density % sol: 46.42 % |
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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 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 % / Av σ(I) over netI: 10.69 / Number: 348771 / Rmerge(I) obs: 0.068 / Χ2: 1.04 / D res high: 2 Å / D res low: 50 Å / Num. obs: 172551 / % possible obs: 84.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2→50 Å / Num. obs: 172551 / % possible obs: 84.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 42.27 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LZG Resolution: 2→49.238 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 1.96 / Phase error: 31.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.254 Å2 / ksol: 0.351 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→49.238 Å
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Refine LS restraints |
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LS refinement shell |
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