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Yorodumi- PDB-4cz0: Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutini... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cz0 | |||||||||
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Title | Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutinin in complex with avian receptor analog Su-3SLN | |||||||||
Components | (HAEMAGGLUTININHemagglutinin) x 2 | |||||||||
Keywords | VIRAL PROTEIN / H10 / SU-3SLN | |||||||||
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: 3.2 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 | 4cz0.cif.gz | 595.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cz0.ent.gz | 499.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/4cz0 ftp://data.pdbj.org/pub/pdb/validation_reports/cz/4cz0 | HTTPS FTP |
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-Related structure data
Related structure data | 4cyvC 4cywC 4cyzC 4d00C 4cvyS 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
#1: Protein | Mass: 34651.934 Da / Num. of mol.: 3 / Fragment: HA1, RESIDUES 18-335 / Source method: isolated from a natural source Source: (natural) INFLUENZA A VIRUS (A/MALLARD/SWEDEN/51/2002 (H10N2)) References: UniProt: E0YNJ7 #2: Protein | Mass: 19774.662 Da / Num. of mol.: 3 / Fragment: HA2, RESIDUES 341-512 / Source method: isolated from a natural source Source: (natural) INFLUENZA A VIRUS (A/MALLARD/SWEDEN/51/2002 (H10N2)) References: UniProt: E0YNJ7 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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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: 3.56 Å3/Da / Density % sol: 65.45 % / 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: 3.2→48.93 Å / Num. obs: 37572 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.4 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CVY Resolution: 3.2→108.04 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.87 / SU B: 101.58 / SU ML: 0.695 / Cross valid method: THROUGHOUT / ESU R Free: 0.57 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 97.393 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→108.04 Å
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Refine LS restraints |
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