[English] 日本語
Yorodumi- PDB-5thb: Crystal structure of H10 hemagglutinin mutant (T193D-Q226L-G228S)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5thb | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of H10 hemagglutinin mutant (T193D-Q226L-G228S) from Jiangxi-Donghu (2013) H10N8 influenza virus | |||||||||
Components | (Hemagglutinin ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / Influenza virus / hemagglutinin / HA / H10N8 (2013) / Receptor specificity | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / 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 / virion membrane Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | |||||||||
Authors | Tzarum, N. / Wilson, I.A. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Cell Rep / Year: 2017 Title: The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Authors: Tzarum, N. / de Vries, R.P. / Peng, W. / Thompson, A.J. / Bouwman, K.M. / McBride, R. / Yu, W. / Zhu, X. / Verheije, M.H. / Paulson, J.C. / Wilson, I.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5thb.cif.gz | 311.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5thb.ent.gz | 249.9 KB | Display | PDB format |
PDBx/mmJSON format | 5thb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5thb_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5thb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5thb_validation.xml.gz | 60 KB | Display | |
Data in CIF | 5thb_validation.cif.gz | 84.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/5thb ftp://data.pdbj.org/pub/pdb/validation_reports/th/5thb | HTTPS FTP |
-Related structure data
Related structure data | 5tgoSC 5tguC 5tgvC 5th0C 5th1C 5thcC 5thfC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Hemagglutinin ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 35284.852 Da / Num. of mol.: 3 / Mutation: D190T, Q223L, G225S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: Jiangxi-Donghu (2013) H10N8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X252, UniProt: A0A059T4A1*PLUS #2: Protein | Mass: 20698.766 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: Jiangxi-Donghu (2013) H10N8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X253, UniProt: A0A059T4A1*PLUS |
---|
-Sugars , 3 types, 7 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 |
---|---|
#4: Polysaccharide | 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: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 637 molecules
#6: Water | ChemComp-HOH / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.86 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M NaCl, 10% (w/v) PEG 8000, 0.1M CHES pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→50 Å / Num. obs: 74001 / % possible obs: 98.1 % / Redundancy: 3.8 % / Rsym value: 0.08 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.41→2.45 Å / % possible obs: 98.5 % / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.7 / CC1/2: 0.942 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TGO Resolution: 2.41→33.055 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.49
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→33.055 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|