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- PDB-5xl3: Complex structure of H4 hemagglutinin from avian influenza H4N6 v... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xl3 | |||||||||
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Title | Complex structure of H4 hemagglutinin from avian influenza H4N6 virus with LSTa | |||||||||
![]() | (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, G.F. | |||||||||
![]() | ![]() 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 | ![]() | 413.3 KB | Display | ![]() |
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PDB format | ![]() | 340.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 42.2 KB | Display | |
Data in CIF | ![]() | 58.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xl1C ![]() 5xl2C ![]() 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
-Protein , 2 types, 4 molecules ABCD
#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: ![]() |
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-Sugars , 3 types, 6 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/SIA.gif)
![](data/chem/img/SIA.gif)
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine | ||
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#4: Sugar | ChemComp-NAG / #5: Sugar | ChemComp-SIA / | |
-Non-polymers , 1 types, 372 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.42 % |
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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: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 68360 / % possible obs: 99.9 % / Redundancy: 10.3 % / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.853 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HA0 Resolution: 2.203→49.091 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.203→49.091 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: -105.5024 Å / Origin y: 202.9967 Å / Origin z: 61.3 Å
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Refinement TLS group | Selection details: all |