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Yorodumi- PDB-3eyk: Structure of Influenza Haemagglutinin in complex with an inhibito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eyk | ||||||
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Title | Structure of Influenza Haemagglutinin in complex with an inhibitor of membrane fusion | ||||||
Components |
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Keywords | VIRAL PROTEIN / Influenza / hemagglutinin / inhibitor / Envelope protein / Fusion protein / Glycoprotein / Lipoprotein / Membrane / Palmitate / Transmembrane / Virion | ||||||
Function / homology | Function and homology information 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 | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Russell, R.J. / Kerry, P.S. / Stevens, D.J. / Steinhauer, D.A. / Martin, S.R. / Gamblin, S.J. / Skehel, J.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: Structure of influenza hemagglutinin in complex with an inhibitor of membrane fusion Authors: Russell, R.J. / Kerry, P.S. / Stevens, D.J. / Steinhauer, D.A. / Martin, S.R. / Gamblin, S.J. / Skehel, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eyk.cif.gz | 116.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eyk.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 3eyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/3eyk ftp://data.pdbj.org/pub/pdb/validation_reports/ey/3eyk | HTTPS FTP |
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-Related structure data
-Links
-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: 35279.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / References: UniProt: P26137 |
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#2: Protein | Mass: 19922.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / References: UniProt: P26137 |
#3: Chemical | ChemComp-EYK / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Tris, PEG8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 29658 / Num. obs: 28412 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.66 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.549 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.307 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.319 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.566 Å / Total num. of bins used: 20
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