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- PDB-4lcx: The structure of hemagglutinin from avian-origin H7N9 influenza v... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lcx | ||||||
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Title | The structure of hemagglutinin from avian-origin H7N9 influenza virus (A/Shanghai/1/2013) | ||||||
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![]() | VIRAL PROTEIN / homotrimer / virus attachment and membrane fusion | ||||||
Function / homology | ![]() 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 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Song, H. / Wu, Y. / Gao, F. / Zhang, Y. / Fan, Z. / Gong, W. ...Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Song, H. / Wu, Y. / Gao, F. / Zhang, Y. / Fan, Z. / Gong, W. / Wang, D. / Shu, Y. / Wang, Y. / Yan, J. / Gao, G.F. | ||||||
![]() | ![]() Title: Structures and receptor binding of hemagglutinins from human-infecting H7N9 influenza viruses. Authors: Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Wu, Y. / Song, H. / Gao, F. / Bi, Y. / Zhang, Y. / Fan, Z. / Qin, C. / Sun, H. / Liu, J. / Haywood, J. / Liu, W. / Gong, W. / Wang, D. / Shu, Y. / ...Authors: Shi, Y. / Zhang, W. / Wang, F. / Qi, J. / Wu, Y. / Song, H. / Gao, F. / Bi, Y. / Zhang, Y. / Fan, Z. / Qin, C. / Sun, H. / Liu, J. / Haywood, J. / Liu, W. / Gong, W. / Wang, D. / Shu, Y. / Wang, Y. / Yan, J. / Gao, G.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 565.8 KB | Display | ![]() |
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PDB format | ![]() | 476.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4kolC ![]() 4komC ![]() 4konC ![]() 4lkgC ![]() 4lkhC ![]() 4lkiC ![]() 4lkjC ![]() 4lkkC 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: 34485.773 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 19634.502 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Sugar | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 18% PEG 8000, 18% Ethylene glycol, 0.12 M Di-Ethyleneglycol, 0.12 M Tri-Ethyleneglycol, 0.12 M TetraEthyleneglycol, 0.12 M Penta-Ethyleneglycol, 0.1 M Tris, 0.1 M Bicine, pH 8.5, VAPOR ...Details: 18% PEG 8000, 18% Ethylene glycol, 0.12 M Di-Ethyleneglycol, 0.12 M Tri-Ethyleneglycol, 0.12 M TetraEthyleneglycol, 0.12 M Penta-Ethyleneglycol, 0.1 M Tris, 0.1 M Bicine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.094→50 Å / Num. all: 39528 / Num. obs: 39468 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 3.1→3.21 Å / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.826 Å2 / ksol: 0.315 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.094→49.882 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -19.0408 Å / Origin y: -10.0818 Å / Origin z: 10.5644 Å
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Refinement TLS group | Selection details: all |