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Yorodumi- PDB-6v46: The crystal structure of hemagglutinin from A/turkey/Ontario/6118... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v46 | |||||||||
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Title | The crystal structure of hemagglutinin from A/turkey/Ontario/6118/1968 (H8N4) | |||||||||
Components | (Hemagglutinin ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / Influenza / avian / H8 | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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: 2.248 Å | |||||||||
Authors | Yang, H. / Stevens, J. | |||||||||
Citation | Journal: Heliyon / Year: 2020 Title: Molecular characterization and three-dimensional structures of avian H8, H11, H14, H15 and swine H4 influenza virus hemagglutinins Authors: Yang, H. / Carney, P.J. / Chang, J. / Stevens, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v46.cif.gz | 600.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v46.ent.gz | 496.5 KB | Display | PDB format |
PDBx/mmJSON format | 6v46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/6v46 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/6v46 | HTTPS FTP |
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-Related structure data
Related structure data | 6v44C 6v47C 6v48C 6v49C 4wsrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER
NCS ensembles :
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-Components
-Hemagglutinin ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 37294.805 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Turkey/Ontario/6118/1968 H8N4) Strain: A/Turkey/Ontario/6118/1968 H8N4 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: F2P175, UniProt: P03456*PLUS #2: Protein | Mass: 20770.014 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Turkey/Ontario/6118/1968 H8N4) Strain: A/Turkey/Ontario/6118/1968 H8N4 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: F2P175, UniProt: P03456*PLUS |
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-Sugars , 3 types, 9 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 1 types, 557 molecules
#6: Water | ChemComp-HOH / |
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-Details
Has ligand of interest | N |
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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: 2.87 Å3/Da / Density % sol: 57.22 % |
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Crystal grow | Temperature: 293 K / Method: microbatch Details: 0.05M Magnesium Chloride, 0.1M HEPES:NaOH pH7.5, 30% (v/v) PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.248→50 Å / Num. obs: 91049 / % possible obs: 98.2 % / Redundancy: 3.8 % / Rsym value: 0.085 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2.25→2.33 Å / Num. unique obs: 4561 / Rsym value: 0.769 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WSR Resolution: 2.248→45.412 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 210.01 Å2 / Biso mean: 47.6987 Å2 / Biso min: 16.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.248→45.412 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 198.4552 Å / Origin y: -40.9481 Å / Origin z: 55.8058 Å
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Refinement TLS group |
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