[English] 日本語
Yorodumi- PDB-4yyb: The structure of hemagglutinin from a H6N1 influenza virus (A/Tai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yyb | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of hemagglutinin from a H6N1 influenza virus (A/Taiwan/2/2013) in complex with human receptor analog 6'SLNLN | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | IMMUNE SYSTEM / Hemagglutinin | ||||||||||||||||||
Function / homology | Function and homology information 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 Similarity search - Function | ||||||||||||||||||
Biological species | unidentified influenza virus | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.609 Å | ||||||||||||||||||
Authors | Wang, F. / Qi, J. / Bi, Y. / Zhang, W. / Wang, M. / Wang, M. / Liu, J. / Yan, J. / Shi, Y. / Gao, G.F. | ||||||||||||||||||
Funding support | China, 5items
| ||||||||||||||||||
Citation | Journal: To Be Published Title: Structure of hemagglutinin from a H6N1 influenza virus (A/Taiwan/2/2013) at 2.6 Angstroms resolution Authors: Wang, F. / Qi, J. / Bi, Y. / Zhang, W. / Wang, M. / Wang, M. / Liu, J. / Yan, J. / Shi, Y. / Gao, G.F. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4yyb.cif.gz | 210.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4yyb.ent.gz | 171.2 KB | Display | PDB format |
PDBx/mmJSON format | 4yyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yyb_validation.pdf.gz | 584.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4yyb_full_validation.pdf.gz | 587.5 KB | Display | |
Data in XML | 4yyb_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 4yyb_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/4yyb ftp://data.pdbj.org/pub/pdb/validation_reports/yy/4yyb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 36548.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified influenza virus Production host: Insect cell expression vector pTIE1 (others) References: UniProt: A0A0J9X268*PLUS |
---|---|
#2: Protein | Mass: 18536.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified influenza virus Production host: Insect cell expression vector pTIE1 (others) References: UniProt: A0A0J9X267*PLUS |
-Sugars , 3 types, 4 molecules
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
---|---|
#4: 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 |
#5: Sugar |
-Non-polymers , 1 types, 91 molecules
#6: Water | ChemComp-HOH / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 5.69 Å3/Da / Density % sol: 78.39 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium acetate, 0.1M sodium acetate pH4.0, 15%(w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.609→50 Å / Num. obs: 37317 / % possible obs: 99.9 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.609→39.774 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.05 / 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: 2.609→39.774 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 40.9197 Å / Origin y: -39.7975 Å / Origin z: -8.1414 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |