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- PDB-5e35: Crystal structure of H5 hemagglutinin mutant (N224K, Q226L, N158D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5.0E+35 | |||||||||
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Title | Crystal structure of H5 hemagglutinin mutant (N224K, Q226L, N158D and L133a deletion) from the influenza virus A/chicken/Vietnam/NCVD-093/2008 (H5N1) with LSTc | |||||||||
![]() | (Hemagglutinin) x 2 | |||||||||
![]() | VIRAL PROTEIN / H5N1 influenza virus / hemagglutinin / receptor binding specificity / transmission / glycan complex | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Zhu, X. / Wilson, I.A. | |||||||||
![]() | ![]() Title: Structural Basis for a Switch in Receptor Binding Specificity of Two H5N1 Hemagglutinin Mutants. Authors: Zhu, X. / Viswanathan, K. / Raman, R. / Yu, W. / Sasisekharan, R. / 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 | ![]() | 118 KB | Display | ![]() |
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PDB format | ![]() | 88.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5e2yC ![]() 5e2zC ![]() 5e30C ![]() 5e32SC ![]() 5e34C 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 37663.824 Da / Num. of mol.: 1 / Fragment: UNP residues 17-346 / Mutation: N224K, Q226L, N158D and L133a deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/chicken/Vietnam/NCVD-093/2008(H5N1) / Gene: HA / Plasmid: PFASTBAC-HT / Production host: ![]() | ||
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#2: Protein | Mass: 20793.016 Da / Num. of mol.: 1 / Fragment: UNP residues 347-521 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine | ||
#4: Sugar | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.6 Å3/Da / Density % sol: 78.03 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M ammonium acetate, 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03314 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 34751 / % possible obs: 97.9 % / Redundancy: 7.4 % / Rsym value: 0.13 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.7→2.76 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.63 / % possible all: 77.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 2.7→46.633 Å
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Refine LS restraints |
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LS refinement shell |
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