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- PDB-6d8b: The crystal structure of hemagglutinin from A/Hong Kong/125/2017 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d8b | ||||||
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Title | The crystal structure of hemagglutinin from A/Hong Kong/125/2017 H7N9 influenza virus | ||||||
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![]() | VIRAL PROTEIN / Influenza / H7N9 | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, H. / Stevens, J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 294.8 KB | Display | ![]() |
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PDB format | ![]() | 239.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 513.1 KB | Display | ![]() |
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Full document | ![]() | 566.2 KB | Display | |
Data in XML | ![]() | 56.9 KB | Display | |
Data in CIF | ![]() | 74.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d7cC ![]() 6d7uC ![]() 6d8dC ![]() 4ln6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35032.613 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 25301.508 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.02 % |
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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: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 48207 / % possible obs: 98.89 % / Redundancy: 3.7 % / Net I/σ(I): 18.39 |
Reflection shell | Resolution: 2.95→3.06 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LN6 Resolution: 2.95→39.154 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→39.154 Å
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Refine LS restraints |
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LS refinement shell |
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