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Yorodumi- PDB-4cyw: Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutini... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cyw | |||||||||
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Title | Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutinin in complex with human receptor analog 6-SLN | |||||||||
Components | (HEMAGGLUTININ) x 2 | |||||||||
Keywords | VIRAL PROTEIN | |||||||||
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: 2.6 Å | |||||||||
Authors | Vachieri, S.G. / Xiong, X. / Collins, P.J. / Walker, P.A. / Martin, S.R. / Haire, L.F. / McCauley, J.W. / Gamblin, S.J. / Skehel, J.J. | |||||||||
Citation | Journal: Nature / Year: 2014 Title: Receptor Binding by H10 Influenza Viruses. Authors: Vachieri, S.G. / Xiong, X. / Collins, P.J. / Walker, P.A. / Martin, S.R. / Haire, L.F. / Zhang, Y. / Mccauley, J.W. / 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 | 4cyw.cif.gz | 603.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cyw.ent.gz | 504.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cyw_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 4cyw_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 4cyw_validation.xml.gz | 55.5 KB | Display | |
Data in CIF | 4cyw_validation.cif.gz | 76.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/4cyw ftp://data.pdbj.org/pub/pdb/validation_reports/cy/4cyw | HTTPS FTP |
-Related structure data
Related structure data | 4cyvSC 4cyzC 4cz0C 4d00C 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
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 35319.750 Da / Num. of mol.: 3 / Fragment: HA1, RESIDUES 17-340 / Source method: isolated from a natural source Source: (natural) INFLUENZA A VIRUS (A/MALLARD/SWEDEN/51/2002 (H10N2)) References: UniProt: E0YNJ7 #2: Protein | Mass: 19887.820 Da / Num. of mol.: 3 / Fragment: HA2, RESIDUES 341-513 / Source method: isolated from a natural source Source: (natural) INFLUENZA A VIRUS (A/MALLARD/SWEDEN/51/2002 (H10N2)) References: UniProt: E0YNJ7 |
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-Sugars , 5 types, 12 molecules
#3: Polysaccharide | #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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 #5: Polysaccharide | beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[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 #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 1 types, 285 molecules
#8: 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: 3.45 Å3/Da / Density % sol: 64.41 % / Description: NONE |
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Crystal grow | Details: 18% PEG 2000MME AND 0.1 M BICINE PH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS / 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: 2.6→48.85 Å / Num. obs: 67905 / % possible obs: 99.1 % / Observed criterion σ(I): 1.8 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.6→2.66 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.8 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CYV Resolution: 2.6→107.72 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 30.236 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 0.481 / ESU R Free: 0.292 / 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: 60.888 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→107.72 Å
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Refine LS restraints |
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