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Yorodumi- PDB-7wl5: Structure of an avian influenza H5 hemagglutinin from the influen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wl5 | ||||||
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Title | Structure of an avian influenza H5 hemagglutinin from the influenza virus A/Equine/Guangxi/25/2010(H5N1) and A/Equine/Guangxi/68/2010(H5N1) | ||||||
Components | (Hemagglutinin) x 2 | ||||||
Keywords | VIRAL PROTEIN / Influenza virus / Haemagglutinin | ||||||
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: 2.8 Å | ||||||
Authors | Wei, X. / Yang, X. / Chen, Q. / Meng, G. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of an avian influenza H5 hemagglutinin from the influenza virus A/Equine/Guangxi/25/2010(H5N1) and A/Equine/Guangxi/68/2010(H5N1) Authors: Wei, X. / Yang, X. / Chen, Q. / Meng, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wl5.cif.gz | 306.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wl5.ent.gz | 251.7 KB | Display | PDB format |
PDBx/mmJSON format | 7wl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/7wl5 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/7wl5 | HTTPS FTP |
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-Related structure data
Related structure data | 6pcxS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 36145.781 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: D1LPE3 #2: Protein | Mass: 19651.666 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A6B7HQ22 |
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-Sugars , 3 types, 15 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #4: Polysaccharide | #5: Sugar | |
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-Non-polymers , 1 types, 20 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: 3.24 Å3/Da / Density % sol: 62.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 3350 and 0.1 M HEPES pH 7.5 |
-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: May 16, 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: 2.8→50 Å / Num. obs: 373309 / % possible obs: 93.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3530 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PCX Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.862 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.468 / 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: 45.206 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→50 Å
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LS refinement shell | Resolution: 2.804→2.877 Å / Total num. of bins used: 20
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