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- PDB-4n5y: Crystal structure of H5 hemagglutinin mutant (N158D, N224K and Q2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4n5y | |||||||||
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Title | Crystal structure of H5 hemagglutinin mutant (N158D, N224K and Q226L) from the influenza virus A/Viet Nam/1203/2004 (H5N1) | |||||||||
![]() | (Hemagglutinin ...) x 2 | |||||||||
![]() | VIRAL PROTEIN / H5N1 / Influenza Virus / hemagglutinin / Ferret transmissible | |||||||||
Function / homology | ![]() 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 / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Zhu, X. / Wilson, I.A. | |||||||||
![]() | ![]() Title: Hemagglutinin Receptor Specificity and Structural Analyses of Respiratory Droplet-Transmissible H5N1 Viruses. Authors: de Vries, R.P. / Zhu, X. / McBride, R. / Rigter, A. / Hanson, A. / Zhong, G. / Hatta, M. / Xu, R. / Yu, W. / Kawaoka, Y. / de Haan, C.A. / Wilson, I.A. / Paulson, J.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7.3 MB | Display | ![]() |
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Full document | ![]() | 7.4 MB | Display | |
Data in XML | ![]() | 235.4 KB | Display | |
Data in CIF | ![]() | 321.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4n5zC ![]() 3gbmS C: citing same article ( S: Starting model for refinement |
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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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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
-Hemagglutinin ... , 2 types, 30 molecules ACEGIKMOQSUWYacBDFHJLNPRTVXZbd
#1: Protein | Mass: 37949.113 Da / Num. of mol.: 15 / Fragment: receptor binding domain, HA1 / Mutation: N158D, N224K, Q226L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 20881.104 Da / Num. of mol.: 15 / Fragment: membrane fusion domain, HA2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 4 types, 29 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 #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: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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 #6: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67.16 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, pH 7.5, 0.2 KF, 22% (w/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 27, 2012 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05876 Å / Relative weight: 1 |
Reflection | Resolution: 3.1615→50 Å / Num. obs: 199766 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rsym value: 0.13 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 3.1615→3.27 Å / % possible all: 83.4 |
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Processing
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Refinement | Method to determine structure: Phaser Starting model: PDB ENTRY 3GBM Resolution: 3.1615→45.283 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29 / 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: 3.1615→45.283 Å
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Refine LS restraints |
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LS refinement shell |
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