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- PDB-6pcx: Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 6.0 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pcx | ||||||
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Title | Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 6.0 | ||||||
![]() | Hemagglutinin | ||||||
![]() | VIRAL PROTEIN / Influenza / H5 | ||||||
Function / homology | ![]() clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Antanasijevic, A. / Durst, M.A. / Lavie, A. / Caffrey, M. | ||||||
![]() | ![]() Title: Identification of a pH sensor in Influenza hemagglutinin using X-ray crystallography. Authors: Antanasijevic, A. / Durst, M.A. / Lavie, A. / Caffrey, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.7 KB | Display | ![]() |
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PDB format | ![]() | 91.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.4 KB | Display | ![]() |
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Full document | ![]() | 487.3 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pd3C ![]() 6pd5C ![]() 6pd6C ![]() 2fk0S 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: 59836.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/mallard/Vietnam/3/2003(H5N1) / Gene: HA / Production host: ![]() | ||||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 70.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM cacodylate, pH 6.0, 200 mM sodium chloride, 2 M ammonium sulfate, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 3, 2016 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→30 Å / Num. obs: 55355 / % possible obs: 99.4 % / Redundancy: 6.44 % / CC1/2: 0.999 / Rrim(I) all: 0.063 / Net I/σ(I): 14.59 |
Reflection shell | Resolution: 2.11→2.22 Å / Redundancy: 6.22 % / Mean I/σ(I) obs: 2.04 / Num. unique obs: 8604 / CC1/2: 0.884 / Rrim(I) all: 0.819 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2FK0 Resolution: 2.11→29.44 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 9.161 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.093 Å2
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Refinement step | Cycle: 1 / Resolution: 2.11→29.44 Å
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Refine LS restraints |
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