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Yorodumi- PDB-4unx: Structure of the A_Equine_Newmarket_2_93 H3 haemagglutinin in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4unx | |||||||||
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Title | Structure of the A_Equine_Newmarket_2_93 H3 haemagglutinin in complex with 3SLN | |||||||||
Components | (H3 HAEMAGGLUTININ ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / EQUINE / CANINE / INFLUENZA / HAEMAGGLUTININ | |||||||||
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 | 4unx.cif.gz | 615.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4unx.ent.gz | 519.7 KB | Display | PDB format |
PDBx/mmJSON format | 4unx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4unx_validation.pdf.gz | 4.3 MB | Display | wwPDB validaton report |
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Full document | 4unx_full_validation.pdf.gz | 4.4 MB | Display | |
Data in XML | 4unx_validation.xml.gz | 54.3 KB | Display | |
Data in CIF | 4unx_validation.cif.gz | 72.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/4unx ftp://data.pdbj.org/pub/pdb/validation_reports/un/4unx | HTTPS FTP |
-Related structure data
Related structure data | 4unwSC 4unyC 4unzC 4uo0C 4uo1C 4uo2C 4uo3C 4uo4C 4uo5C 4uo6C 4uo7C 4uo8C 4uo9C 4uoaC 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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Unit cell |
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-Components
-H3 HAEMAGGLUTININ ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 35867.383 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS (A/EQ/NEWMARKET/93/(H3N8)) Description: ANIMAL HEALTH TRUST, NEWMARKET, UNITED KINGDOM / Plasmid: PACGP67 DERIVATIVE / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q82847 #2: Protein | Mass: 19968.105 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS (A/EQ/NEWMARKET/93/(H3N8)) Description: ANIMAL HEALTH TRUST, NEWMARKET, UNITED KINGDOM / Plasmid: PACGP67 DERIVATIVE / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) |
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-Sugars , 7 types, 20 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 | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine | #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-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 | ChemComp-NAG / #9: Sugar | |
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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: 3.59 Å3/Da / Density % sol: 65.74 % / 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: 3.2→52.24 Å / Num. obs: 39591 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UNW Resolution: 3.2→114.19 Å / Cor.coef. Fo:Fc: 0.82 / Cor.coef. Fo:Fc free: 0.768 / SU B: 111.536 / SU ML: 0.793 / Cross valid method: THROUGHOUT / ESU R Free: 0.661 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. 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: 109.722 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→114.19 Å
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Refine LS restraints |
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