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Yorodumi- PDB-3al4: Crystal structure of the swine-origin A (H1N1)-2009 influenza A v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3al4 | ||||||||||||
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Title | Crystal structure of the swine-origin A (H1N1)-2009 influenza A virus hemagglutinin (HA) reveals similar antigenicity to that of the 1918 pandemic virus | ||||||||||||
Components | (Hemagglutinin) x 2 | ||||||||||||
Keywords | VIRAL PROTEIN/VIRAL PROTEIN / TRIMER / ENVELOPE PROTEIN / HEMAGGLUTININ / VIRAL PROTEIN-VIRAL PROTEIN 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 | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.872 Å | ||||||||||||
Authors | Zhang, W. / Qi, J.X. / Shi, Y. / Li, Q. / Yan, J.H. / Gao, G.F. | ||||||||||||
Citation | Journal: Protein Cell / Year: 2010 Title: Crystal structure of the swine-origin A (H1N1)-2009 influenza A virus hemagglutinin (HA) reveals similar antigenicity to that of the 1918 pandemic virus Authors: Zhang, W. / Qi, J. / Shi, Y. / Li, Q. / Gao, F. / Sun, Y. / Lu, X. / Lu, Q. / Vavricka, C.J. / Liu, D. / Yan, J. / Gao, G.F. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3al4.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3al4.ent.gz | 984.7 KB | Display | PDB format |
PDBx/mmJSON format | 3al4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/3al4 ftp://data.pdbj.org/pub/pdb/validation_reports/al/3al4 | HTTPS FTP |
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-Related structure data
Related structure data | 1ru7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein | Mass: 36989.715 Da / Num. of mol.: 6 / Fragment: UNP residues 18-344 Source method: isolated from a genetically manipulated source Details: HEMAGGLUTININ HA1 / Source: (gene. exp.) Influenza A virus / Strain: A/CALIFORNIA/04/2009(H1N1) / Gene: HEMAGGLUTININ / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: C3W5S1 #2: Protein | Mass: 20757.035 Da / Num. of mol.: 6 / Fragment: UNP residues 345-520 Source method: isolated from a genetically manipulated source Details: HEMAGGLUTININ HA2 / Source: (gene. exp.) Influenza A virus / Strain: A/CALIFORNIA/04/2009(H1N1) / Gene: HEMAGGLUTININ / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: C3W5S1 |
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-Sugars , 3 types, 23 molecules
#3: 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 #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 1 types, 317 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: 2.18 Å3/Da / Density % sol: 43.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG 6000, 5% MPD, 0.1M MES, 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: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2010 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.872→50 Å / Num. obs: 64796 / % possible obs: 98 % / Observed criterion σ(I): 1.5 / Redundancy: 3.7 % / Biso Wilson estimate: 56.27 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.87→3 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.501 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RU7 Resolution: 2.872→24.19 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / σ(F): 0.07 / Phase error: 29.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.94 Å2 / ksol: 0.29 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 330.34 Å2 / Biso mean: 81.17 Å2 / Biso min: 16.64 Å2
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Refinement step | Cycle: LAST / Resolution: 2.872→24.19 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -20.2272 Å / Origin y: -28.1217 Å / Origin z: -32.6646 Å
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Refinement TLS group |
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