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Yorodumi- PDB-2ypg: Haemagglutinin of 1968 Human H3N2 Virus in Complex with Human Rec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ypg | |||||||||
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Title | Haemagglutinin of 1968 Human H3N2 Virus in Complex with Human Receptor Analogue LSTc | |||||||||
Components | (HEMAGGLUTININ ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / RECEPTOR BINDING / MEMBRANE FUSION / INFLUENZA VIRUS EVOLUTION / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / membrane Similarity search - Function | |||||||||
Biological species | INFLUENZA A VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Liu, J. / Xiong, X. / Haire, L.F. / Lin, Y.P. / Wharton, S.A. / Martin, S.R. / Coombs, P.J. / Vachieri, S.G. / Christodoulou, E. / Walker, P.A. ...Liu, J. / Xiong, X. / Haire, L.F. / Lin, Y.P. / Wharton, S.A. / Martin, S.R. / Coombs, P.J. / Vachieri, S.G. / Christodoulou, E. / Walker, P.A. / Skehel, J.J. / Gamblin, S.J. / Hay, A.J. / Daniels, R.S. / McCauley, J.W. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Evolution of the Receptor Binding Properties of the Influenza A(H3N2) Hemagglutinin. Authors: Lin, Y.P. / Xiong, X. / Wharton, S.A. / Martin, S.R. / Coombs, P.J. / Vachieri, S.G. / Christodoulou, E. / Walker, P.A. / Liu, J. / Skehel, J.J. / Gamblin, S.J. / Hay, A.J. / Daniels, R.S. / Mccauley, J.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ypg.cif.gz | 605.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ypg.ent.gz | 507.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ypg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ypg_validation.pdf.gz | 4.2 MB | Display | wwPDB validaton report |
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Full document | 2ypg_full_validation.pdf.gz | 4.2 MB | Display | |
Data in XML | 2ypg_validation.xml.gz | 70.7 KB | Display | |
Data in CIF | 2ypg_validation.cif.gz | 90.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/2ypg ftp://data.pdbj.org/pub/pdb/validation_reports/yp/2ypg | HTTPS FTP |
-Related structure data
Related structure data | 2yp2C 2yp3C 2yp4C 2yp5C 2yp7C 2yp8C 2yp9C 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
-HEMAGGLUTININ ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 36065.457 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) INFLUENZA A VIRUS (A/X-31(H3N2)) / References: UniProt: P03437 #2: Protein | Mass: 20212.350 Da / Num. of mol.: 3 Fragment: HA2 OF BROMELAIN RELEASED ECTODOMAIN, RESIDUES 346-520 Source method: isolated from a natural source / Source: (natural) INFLUENZA A VIRUS (A/X-31(H3N2)) / References: UniProt: P03437 |
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-Sugars , 7 types, 17 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||||
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#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: 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 #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #8: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 446 molecules
#10: Chemical | ChemComp-FLC / #11: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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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: 6.42 Å3/Da / Density % sol: 80.7 % / Description: NONE |
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Crystal grow | Details: 1.7-2 M TRIAMMONIUM CITRATE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979492 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979492 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→177.21 Å / Num. obs: 104897 / % possible obs: 100 % / Observed criterion σ(I): 2.7 / Redundancy: 6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→160.77 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.933 / SU B: 13.478 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 39.986 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→160.77 Å
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