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- PDB-5xl1: The structure of hemagglutinin from an avian-origin H4N6 influenz... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xl1 | ||||||
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Title | The structure of hemagglutinin from an avian-origin H4N6 influenza virus | ||||||
![]() | (Hemagglutinin) x 2 | ||||||
![]() | VIRAL PROTEIN / H4 hemagglutinin / influenza virus / receptor binding | ||||||
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 / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Song, H. / Qi, J. / Gao, F.G. | ||||||
![]() | ![]() Title: Avian-to-Human Receptor-Binding Adaptation by Influenza A Virus Hemagglutinin H4 Authors: Song, H. / Qi, J. / Xiao, H. / Bi, Y. / Zhang, W. / Xu, Y. / Wang, F. / Shi, Y. / 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 | ![]() | 405.1 KB | Display | ![]() |
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PDB format | ![]() | 332 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.8 KB | Display | ![]() |
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Full document | ![]() | 488.5 KB | Display | |
Data in XML | ![]() | 40.5 KB | Display | |
Data in CIF | ![]() | 58 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xl2C ![]() 5xl3C ![]() 5xl4C ![]() 5xl5C ![]() 5xl6C ![]() 5xl7C ![]() 5xl8C ![]() 5xl9C ![]() 5xlaC ![]() 5xlbC ![]() 5xlcC ![]() 5xldC ![]() 1ha0S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 35966.461 Da / Num. of mol.: 2 / Fragment: UNP residues 17-343 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: ![]() #2: Protein | Mass: 20342.391 Da / Num. of mol.: 2 / Fragment: UNP residues 344-519 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: ![]() #3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Trimethylamine N-oxide dehydrate, 0.1 M Tris (pH 8.0), and 20% PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 60221 / % possible obs: 100 % / Redundancy: 9 % / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.686 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HA0 Resolution: 2.3→43.42 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→43.42 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: -73.1146 Å / Origin y: 163.8395 Å / Origin z: 61.5862 Å
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Refinement TLS group | Selection details: all |