[English] 日本語
Yorodumi- PDB-4we4: The crystal structure of hemagglutinin from 1968 H3N2 influenza virus -
+Open data
-Basic information
Entry | Database: PDB / ID: 4we4 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The crystal structure of hemagglutinin from 1968 H3N2 influenza virus | ||||||||||||
Components | (Hemagglutinin ...) x 2 | ||||||||||||
Keywords | VIRAL PROTEIN / Hemagglutinin / H3 / influenza virus | ||||||||||||
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 / Resolution: 2.351 Å | ||||||||||||
Authors | Yang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J. | ||||||||||||
Citation | Journal: Virology / Year: 2015 Title: Structure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins. Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4we4.cif.gz | 129.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4we4.ent.gz | 97.6 KB | Display | PDB format |
PDBx/mmJSON format | 4we4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/4we4 ftp://data.pdbj.org/pub/pdb/validation_reports/we/4we4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4we5C 4we6C 4we7C 4we8C 4we9C 4weaC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Hemagglutinin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 35339.758 Da / Num. of mol.: 1 / Fragment: unp residues 25-345 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7 |
---|---|
#2: Protein | Mass: 19911.973 Da / Num. of mol.: 1 / Fragment: unp residues 346-517 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7 |
-Sugars , 5 types, 6 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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 |
---|---|
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 |
#5: 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 |
#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#7: Sugar |
-Non-polymers , 3 types, 308 molecules
#8: Chemical | ChemComp-PEG / #9: Chemical | ChemComp-PE5 / | #10: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.63 % |
---|---|
Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7.9 / Details: 0.1M Tris-HCl, 25% PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 25624 / % possible obs: 98.1 % / Redundancy: 10.8 % / Net I/σ(I): 40 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.351→30.497 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.95 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.351→30.497 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|