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Yorodumi- PDB-4uo1: Structure of the A_Equine_Richmond_07 H3 haemagglutinin in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uo1 | |||||||||
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Title | Structure of the A_Equine_Richmond_07 H3 haemagglutinin in complex with 3SLN | |||||||||
Components | (HEMAGGLUTININ) x 2 | |||||||||
Keywords | VIRAL PROTEIN / EQUINE / INFLUENZA | |||||||||
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: 3 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 | 4uo1.cif.gz | 624.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uo1.ent.gz | 524.8 KB | Display | PDB format |
PDBx/mmJSON format | 4uo1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uo1_validation.pdf.gz | 4.7 MB | Display | wwPDB validaton report |
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Full document | 4uo1_full_validation.pdf.gz | 4.7 MB | Display | |
Data in XML | 4uo1_validation.xml.gz | 53.4 KB | Display | |
Data in CIF | 4uo1_validation.cif.gz | 72.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/4uo1 ftp://data.pdbj.org/pub/pdb/validation_reports/uo/4uo1 | HTTPS FTP |
-Related structure data
Related structure data | 4unwC 4unxC 4unyC 4unzC 4uo0SC 4uo2C 4uo3C 4uo4C 4uo5C 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
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 36640.312 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS (A/EQUINE/RICHMOND/1/2007)(H3N8)) Description: ANIMAL HEALTH TRUST, NEWMARKET, UNITED KINGDOM / Plasmid: PACGP67 DERIVATIVE / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: C3TUR9 #2: Protein | Mass: 19957.035 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS (A/EQUINE/RICHMOND/1/2007)(H3N8)) Description: ANIMAL HEALTH TRUST, NEWMARKET, UNITED KINGDOM / Plasmid: PACGP67 DERIVATIVE / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: C3TUR9 |
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-Sugars , 10 types, 23 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 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: 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 #7: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #8: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #9: Polysaccharide | #10: Polysaccharide | Source method: isolated from a genetically manipulated source #11: Sugar | ChemComp-NAG / #12: Sugar | ChemComp-FUC / | |
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-Non-polymers , 1 types, 71 molecules
#13: 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: 2.96 Å3/Da / Density % sol: 58.54 % / 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: 3→108 Å / Num. obs: 39675 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.33 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.95 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UO0 Resolution: 3→107.98 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.821 / SU B: 90.208 / SU ML: 0.669 / Cross valid method: THROUGHOUT / ESU R Free: 0.588 / 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: 81.449 Å2
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Refinement step | Cycle: LAST / Resolution: 3→107.98 Å
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Refine LS restraints |
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