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- PDB-5thf: Crystal structure of H3 hemagglutinin with insertion of two amino... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5thf | |||||||||
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Title | Crystal structure of H3 hemagglutinin with insertion of two amino acids in the 150-loop from the A/Hong Kong/1/1968 (H3N2) influenza virus | |||||||||
![]() | (Hemagglutinin ...) x 2 | |||||||||
![]() | VIRAL PROTEIN / Influenza virus / hemagglutinin / HA / H10N8 (2013) / Receptor specificity | |||||||||
Function / homology | ![]() viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 | ![]() ![]() ![]() | |||||||||
![]() | Tzarum, N. / Wilson, I.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Authors: Tzarum, N. / de Vries, R.P. / Peng, W. / Thompson, A.J. / Bouwman, K.M. / McBride, R. / Yu, W. / Zhu, X. / Verheije, M.H. / Paulson, J.C. / Wilson, I.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 309.3 KB | Display | ![]() |
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PDB format | ![]() | 250.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 57.5 KB | Display | |
Data in CIF | ![]() | 79.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tgoC ![]() 5tguC ![]() 5tgvC ![]() 5th0C ![]() 5th1C ![]() 5thbC ![]() 5thcC ![]() 4fnkS 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
-Hemagglutinin ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 35723.203 Da / Num. of mol.: 3 / Mutation: Insertion Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: ![]() #2: Protein | Mass: 20854.945 Da / Num. of mol.: 3 / Mutation: R468G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 10 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 1 types, 370 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: 3.12 Å3/Da / Density % sol: 60.62 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% (w/v) PEG 3500, 0.2M Na2HPO4 pH 9.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 64033 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rsym value: 0.16 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.2 / CC1/2: 0.67 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FNK Resolution: 2.59→48.601 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→48.601 Å
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Refine LS restraints |
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LS refinement shell |
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