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Yorodumi- PDB-4uo9: Structure of the A_Canine_Colorado_17864_06 H3 haemagglutinin Ser... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uo9 | |||||||||
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Title | Structure of the A_Canine_Colorado_17864_06 H3 haemagglutinin Ser30Thr mutant | |||||||||
Components |
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Keywords | VIRAL PROTEIN / EQUINE / INFLUENZA | |||||||||
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 | INFLUENZA A VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | |||||||||
Authors | Vachieri, S.G. / Collins, P.J. / Haire, L.F. / Ogrodowicz, R.W. / Martin, S.R. / Walker, P.A. / Xiong, X. / Gamblin, S.J. / Skehel, J.J. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Recent Evolution of Equine Influenza and the Origin of Canine Influenza. Authors: Collins, P.J. / Vachieri, S.G. / Haire, L.F. / Ogrodowicz, R.W. / Martin, S.R. / Walker, P.A. / Xiong, X. / Gamblin, S.J. / Skehel, J.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uo9.cif.gz | 214.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uo9.ent.gz | 174.2 KB | Display | PDB format |
PDBx/mmJSON format | 4uo9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/4uo9 ftp://data.pdbj.org/pub/pdb/validation_reports/uo/4uo9 | HTTPS FTP |
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-Related structure data
Related structure data | 4unwC 4unxC 4unyC 4unzC 4uo0C 4uo1C 4uo2C 4uo3C 4uo4SC 4uo5C 4uo6C 4uo7C 4uo8C 4uoaC 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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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 36360.012 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS (A/CANINE/COLORADO/17864/2006(H3N8)) Description: DR. EDWARD J. DUBOVI AND DR. COLIN PARRISH, CORNELL UNIVERSITY, ITHACA, NY, USA Plasmid: PACGP67 DERIVATIVE / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: E0UVR5 |
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#2: Protein | Mass: 20273.373 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS (A/CANINE/COLORADO/17864/2006(H3N8)) Description: DR. EDWARD J. DUBOVI AND DR. COLIN PARRISH, CORNELL UNIVERSITY, ITHACA, NY, USA Plasmid: PACGP67 DERIVATIVE / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: E0UVR5 |
-Sugars , 3 types, 5 molecules
#3: Polysaccharide | 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 | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | |
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-Non-polymers , 2 types, 5 molecules
#6: Chemical | #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: 3.46 Å3/Da / Density % sol: 64.45 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→46.97 Å / Num. obs: 12600 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 3.2→3.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UO4 Resolution: 3.2→132.18 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.874 / SU B: 55.798 / SU ML: 0.411 / Cross valid method: THROUGHOUT / ESU R Free: 0.524 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.193 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→132.18 Å
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Refine LS restraints |
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