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Yorodumi- PDB-5tg9: Crystal structure of H15 hemagglutinin from A/shearwater/WA/2576/... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tg9 | |||||||||
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Title | Crystal structure of H15 hemagglutinin from A/shearwater/WA/2576/1979 H15N9 influenza virus in complex with 3'-SLN | |||||||||
Components |
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Keywords | VIRAL PROTEIN / Influenza virus / hemagglutinin / HA / H15N9 / 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: 2.749 Å | |||||||||
Authors | Wilson, I.A. / Tzarum, N. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Virol. / Year: 2017 Title: Unique Structural Features of Influenza Virus H15 Hemagglutinin. Authors: Tzarum, N. / McBride, R. / Nycholat, C.M. / Peng, W. / Paulson, J.C. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tg9.cif.gz | 213.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tg9.ent.gz | 168 KB | Display | PDB format |
PDBx/mmJSON format | 5tg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tg9_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5tg9_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5tg9_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 5tg9_validation.cif.gz | 53.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/5tg9 ftp://data.pdbj.org/pub/pdb/validation_reports/tg/5tg9 | HTTPS FTP |
-Related structure data
Related structure data | 5tg8SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 36210.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/shearWater/Australia/2576/1979(H15N9)) Strain: A/shearWater/Australia/2576/1979(H15N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: L0L3X3 #2: Protein | Mass: 22210.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/shearWater/Australia/2576/1979(H15N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: L0L3X3 |
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-Sugars , 4 types, 6 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine | #6: Sugar | |
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-Non-polymers , 1 types, 105 molecules
#7: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.25 Å3/Da / Density % sol: 71.04 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% (w/v) PEG 3500, 0.2M potassium nitrate pH 6.9. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 79813 / % possible obs: 97.4 % / Redundancy: 2.7 % / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.75→2.8 Å / % possible obs: 99.3 % / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.522 / Rsym value: 0.99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TG8 Resolution: 2.749→43.283 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.749→43.283 Å
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Refine LS restraints |
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LS refinement shell |
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