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Yorodumi- PDB-7dea: Structure of an avian influenza H5 hemagglutinin from the influen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dea | ||||||
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Title | Structure of an avian influenza H5 hemagglutinin from the influenza virus A/duck Northern China/22/2017 (H5N6) | ||||||
Components | (Hemagglutinin) x 2 | ||||||
Keywords | VIRAL PROTEIN / H5N6 avian influenza virus / Haemagglutinin / Neuraminidase / Acid stability / Human infection | ||||||
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: 2.84 Å | ||||||
Authors | Sun, H. / Sun, H. / Song, J. / Zhang, W. / Wei, X. / Qi, J. / Gao, G.F. / Liu, J. | ||||||
Citation | Journal: To Be Published Title: Haemagglutinin and neuraminidase acid stability in H5N6 avian influenza virus confers infection adaptation in mammals Authors: Sun, H. / Sun, H. / Song, J. / Zhang, W. / Qi, J. / Gao, G.F. / Liu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dea.cif.gz | 300.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dea.ent.gz | 245.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dea_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 7dea_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 7dea_validation.xml.gz | 52.1 KB | Display | |
Data in CIF | 7dea_validation.cif.gz | 69.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/7dea ftp://data.pdbj.org/pub/pdb/validation_reports/de/7dea | HTTPS FTP |
-Related structure data
Related structure data | 7debC 6ntfS 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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-Components
#1: Protein | Mass: 36169.898 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA Production host: Insect cell expression vector pTIE1 (others) #2: Protein | Mass: 19883.906 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA Production host: Insect cell expression vector pTIE1 (others) References: UniProt: A0A6M2RI35 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 4.08 Å3/Da / Density % sol: 69.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→135.91 Å / Num. obs: 65192 / % possible obs: 99.66 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.7→2.85 Å / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3762 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NTF Resolution: 2.84→135.91 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||
Displacement parameters | Biso mean: 70.243 Å2
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Refinement step | Cycle: 1 / Resolution: 2.84→135.91 Å
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LS refinement shell | Resolution: 2.843→2.917 Å / Total num. of bins used: 20
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