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Yorodumi- PDB-7deb: Structure of an avian influenza H5 hemagglutinin from the influen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7deb | ||||||
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Title | Structure of an avian influenza H5 hemagglutinin from the influenza virus A/duck/Eastern China/L0230/2010 (H5N2) | ||||||
Components | Hemagglutinin | ||||||
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: 2.6 Å | ||||||
Authors | Sun, H. / Sun, H. / Song, J. / Zhang, W. / 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 | 7deb.cif.gz | 316 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7deb.ent.gz | 256.7 KB | Display | PDB format |
PDBx/mmJSON format | 7deb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7deb_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7deb_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7deb_validation.xml.gz | 58.6 KB | Display | |
Data in CIF | 7deb_validation.cif.gz | 81.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/7deb ftp://data.pdbj.org/pub/pdb/validation_reports/de/7deb | HTTPS FTP |
-Related structure data
Related structure data | 7deaC 4nfdS 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: 57617.762 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/duck/Eastern China/L0321/2010(H5N2)) Strain: A/duck/Eastern China/L0321/2010(H5N2) / Gene: HA Production host: Insect cell expression vector pTIE1 (others) References: UniProt: A0A0X7YU24 #2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | #5: Water | ChemComp-HOH / | 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: 5.21 Å3/Da / Density % sol: 76.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium nitrate, 20% w/v Polyethylene glycol 3,350 |
-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: Nov 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 111361 / % possible obs: 99.52 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 4 / Num. unique obs: 10993 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NFD Resolution: 2.6→46.58 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.919 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.217 / 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: 49.14 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→46.58 Å
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LS refinement shell | Resolution: 2.6→2.665 Å
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