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Yorodumi- PDB-6d8d: The crystal structure of hemagglutinin from A/Hong Kong/125/2017 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d8d | |||||||||
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Title | The crystal structure of hemagglutinin from A/Hong Kong/125/2017 influenza virus in complex with LSTb | |||||||||
Components | (Hemagglutinin ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / Influenza / H7N9 | |||||||||
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: 3.55 Å | |||||||||
Authors | Yang, H. / Stevens, J. | |||||||||
Citation | Journal: J. Virol. / Year: 2018 Title: Structural and Molecular Characterization of the Hemagglutinin from the Fifth-Epidemic-Wave A(H7N9) Influenza Viruses. Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Stevens, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d8d.cif.gz | 585.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d8d.ent.gz | 488.3 KB | Display | PDB format |
PDBx/mmJSON format | 6d8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/6d8d ftp://data.pdbj.org/pub/pdb/validation_reports/d8/6d8d | HTTPS FTP |
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-Related structure data
Related structure data | 6d7cC 6d7uC 6d8bC 4ln6S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
-Hemagglutinin ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 35032.613 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/125/2017 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A2I7YV81 #2: Protein | Mass: 25301.508 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/125/2017 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A218MY65 |
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-Sugars , 5 types, 13 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / #6: Sugar | #7: Sugar | ChemComp-SIA / | |
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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: 3.28 Å3/Da / Density % sol: 62.56 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / Details: 0.2M Magnesium Acetate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.55→50 Å / Num. obs: 26155 / % possible obs: 99.7 % / Redundancy: 3.7 % / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 3.55→3.68 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LN6 Resolution: 3.55→50.01 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.846 / SU B: 79.537 / SU ML: 0.502 / Cross valid method: THROUGHOUT / ESU R Free: 0.662 / 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: 69.546 Å2
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Refinement step | Cycle: 1 / Resolution: 3.55→50.01 Å
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Refine LS restraints |
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