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Yorodumi- PDB-4uo5: Structure of the A_Canine_Colorado_17864_06 H3 haemagglutinin in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uo5 | |||||||||
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Title | Structure of the A_Canine_Colorado_17864_06 H3 haemagglutinin in complex with 3SLN | |||||||||
Components | (H3 HAEMAGGLUTININ ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN | |||||||||
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: 2.7 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 | 4uo5.cif.gz | 624 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uo5.ent.gz | 524.2 KB | Display | PDB format |
PDBx/mmJSON format | 4uo5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/4uo5 ftp://data.pdbj.org/pub/pdb/validation_reports/uo/4uo5 | HTTPS FTP |
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-Related structure data
Related structure data | 4unwC 4unxC 4unyC 4unzC 4uo0C 4uo1C 4uo2C 4uo3C 4uo4SC 4uo6C 4uo7C 4uo8C 4uo9C 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 on special symmetry positions |
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-Components
-H3 HAEMAGGLUTININ ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 36345.984 Da / Num. of mol.: 3 / Fragment: RESIDUES 345-516 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/CANINE/COLORADO/17864/2006(H3N8) Description: DR. EDWARD J. DUBOVI AND DR. COLIN PARRISH, CORNELL UNIVERSITY, ITHACA, NY, USA Plasmid: PACGP67 DERIVATIVE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: E0UVR5 #2: Protein | Mass: 20273.373 Da / Num. of mol.: 3 / Fragment: RESIDUES 17-344 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/CANINE/COLORADO/17864/2006(H3N8) Description: DR. EDWARD J. DUBOVI AND DR. COLIN PARRISH, CORNELL UNIVERSITY, ITHACA, NY, USA Plasmid: PACGP67 DERIVATIVE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: E0UVR5 |
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-Sugars , 6 types, 17 molecules
#3: 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 #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | #7: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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 #8: Sugar | |
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-Non-polymers , 2 types, 125 molecules
#9: Chemical | #10: 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: 4.26 Å3/Da / Density % sol: 71.17 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→47.82 Å / Num. obs: 75251 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.3 / % possible all: 98 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UO4 Resolution: 2.7→174.58 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 23.725 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.417 / ESU R Free: 0.266 / 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: 72.049 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→174.58 Å
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Refine LS restraints |
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