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Yorodumi- PDB-1z50: Parainfluenza Virus 5 (SV5) Hemagglutinin-Neuraminidase (HN) with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z50 | |||||||||
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Title | Parainfluenza Virus 5 (SV5) Hemagglutinin-Neuraminidase (HN) with ligand DANA (soaked with sialic acid, pH 8.0) | |||||||||
Components | Hemagglutinin-neuraminidase | |||||||||
Keywords | HYDROLASE / hemagglutinin / neuraminidase / fusion / tetramer | |||||||||
Function / homology | Function and homology information exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane ...exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Simian virus 5 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Yuan, P. / Thompson, T.B. / Wurzburg, B.A. / Paterson, R.G. / Lamb, R.A. / Jardetzky, T.S. | |||||||||
Citation | Journal: Structure / Year: 2005 Title: Structural studies of the parainfluenza virus 5 hemagglutinin-neuraminidase tetramer in complex with its receptor, sialyllactose. Authors: Yuan, P. / Thompson, T.B. / Wurzburg, B.A. / Paterson, R.G. / Lamb, R.A. / Jardetzky, T.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z50.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z50.ent.gz | 82.2 KB | Display | PDB format |
PDBx/mmJSON format | 1z50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z50_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1z50_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 1z50_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 1z50_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/1z50 ftp://data.pdbj.org/pub/pdb/validation_reports/z5/1z50 | HTTPS FTP |
-Related structure data
Related structure data | 1z4vC 1z4wC 1z4xC 1z4yC 1z4zC 1e8tS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 58508.812 Da / Num. of mol.: 1 / Fragment: Extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian virus 5 / Genus: Rubulavirus / Strain: W3 / Gene: HN / Plasmid: pBacgus-3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04850, exo-alpha-sialidase |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / | #5: Sugar | ChemComp-DAN / | |
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-Non-polymers , 2 types, 197 molecules
#4: Chemical | ChemComp-CA / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.34 Å3/Da / Density % sol: 71.6 % |
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Crystal grow | Temperature: 291 K / Method: hanging drop / pH: 8 Details: PEG 2000 MME, NaCl, Tris, pH 8.0, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9918 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 26160 / % possible obs: 100 % / Rmerge(I) obs: 0.119 / Χ2: 1.008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1E8T Resolution: 2.8→50 Å / σ(F): 0
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Solvent computation | Bsol: 33.539 Å2 | ||||||||||||||||||||
Displacement parameters | Biso mean: 27.598 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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Xplor file |
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