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- PDB-4cyv: Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutinin -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cyv | |||||||||
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Title | Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutinin | |||||||||
![]() | (HEMAGGLUTININ) x 2 | |||||||||
![]() | VIRAL PROTEIN | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 602.5 KB | Display | ![]() |
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PDB format | ![]() | 502.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 60.5 KB | Display | |
Data in CIF | ![]() | 82.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cywC ![]() 4cyzC ![]() 4cz0C ![]() 4d00C ![]() 1ti8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() References: UniProt: E0YNJ7 #2: Protein | Mass: 19774.662 Da / Num. of mol.: 3 / Fragment: HA2, RESIDUES 341-513 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: E0YNJ7 |
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-Sugars , 4 types, 11 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: 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 #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: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 323 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.16 % / 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: ![]() ![]() ![]() |
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: 2.3→49.15 Å / Num. obs: 84779 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TI8 Resolution: 2.3→113.99 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 17.345 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.23 / 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: 57.075 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→113.99 Å
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Refine LS restraints |
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