[English] 日本語
Yorodumi- PDB-3eym: Structure of Influenza Haemagglutinin in complex with an inhibito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eym | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Influenza Haemagglutinin in complex with an inhibitor of membrane fusion | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN / Influenza / hemagglutinin / inhibitor / Envelope protein / Fusion protein / Glycoprotein / Lipoprotein / Membrane / Palmitate / Transmembrane / Virion | ||||||
Function / homology | Function and homology information viral budding from plasma membrane / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Russell, R.J. / Kerry, P.S. / Stevens, D.A. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3eym.cif.gz | 287.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3eym.ent.gz | 235.5 KB | Display | PDB format |
PDBx/mmJSON format | 3eym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/3eym ftp://data.pdbj.org/pub/pdb/validation_reports/ey/3eym | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35368.824 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / References: UniProt: P03437 #2: Protein | Mass: 19912.959 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / References: UniProt: P03437 #3: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium citratre, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97565 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 9, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97565 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→129 Å / Num. all: 104202 / Num. obs: 103890 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.8→2.93 Å / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.93 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.095 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 57.576 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
|