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- PDB-5th0: Crystal structure of H10 hemagglutinin mutant (K158aA-Q226L-G228S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5th0 | |||||||||
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Title | Crystal structure of H10 hemagglutinin mutant (K158aA-Q226L-G228S) from Jiangxi-Donghu (2013) H10N8 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 / 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 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 | ![]() | 309.9 KB | Display | ![]() |
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PDB format | ![]() | 249.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5tgoSC ![]() 5tguC ![]() 5tgvC ![]() 5th1C ![]() 5thbC ![]() 5thcC ![]() 5thfC 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: 35240.734 Da / Num. of mol.: 3 / Mutation: K154A, Q223L, G225S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 20698.766 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 6 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 611 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: 3.2 Å3/Da / Density % sol: 61.56 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M NaCl, 10% (w/v) PEG 8000, 0.1M CHES pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 95403 / % possible obs: 94.8 % / Redundancy: 3 % / Rsym value: 0.17 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.25→2.29 Å / % possible obs: 97.8 % / Redundancy: 3 % / Mean I/σ(I) obs: 3.2 / CC1/2: 0.354 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TGO Resolution: 2.25→48.967 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→48.967 Å
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Refine LS restraints |
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LS refinement shell |
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