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- PDB-4lkh: The structure of hemagglutinin from a avian-origin H7N9 influenza... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lkh | ||||||
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Title | The structure of hemagglutinin from a avian-origin H7N9 influenza virus (A/Shanghai/1/2013) in complex with human receptor analog 6'SLNLN | ||||||
![]() | (hemagglutinin) x 2 | ||||||
![]() | VIRAL PROTEIN / homotrimer / virus attachment / 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 | ![]() | 208.8 KB | Display | ![]() |
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PDB format | ![]() | 168.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 774.3 KB | Display | ![]() |
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Full document | ![]() | 780.8 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kolC ![]() 4komC ![]() 4konC ![]() 4lcxC ![]() 4lkgC ![]() 4lkiC ![]() 4lkjC ![]() 4lkkC ![]() 4dj6S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34485.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 19634.502 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Sugar | #4: Sugar | ChemComp-SIA / | Sequence details | THE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN WHICH DERIVED FROM STRAIN A/SHANGHAI/1/2013 DOES ...THE SEQUENCE DATABASE REFERENCES | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M ammonium citrate tribasic, 20%(w/v) Polyethylene glycol 3350, pH 7.0, 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: Jul 2, 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: 3.099→50 Å / Num. all: 14322 / Num. obs: 14311 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 80.04 Å2 |
Reflection shell | Resolution: 3.1→3.21 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DJ6 Resolution: 3.099→47.688 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8 / SU ML: 0.28 / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.867 Å2 / ksol: 0.287 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 221.94 Å2 / Biso mean: 108.9378 Å2 / Biso min: 37.57 Å2
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Refinement step | Cycle: LAST / Resolution: 3.099→47.688 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 11.1634 Å / Origin y: 11.7624 Å / Origin z: 57.4185 Å
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Refinement TLS group | Selection details: ALL |