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- PDB-6tvd: Crystal structure of the haemagglutinin from a H10N7 seal influen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tvd | ||||||
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Title | Crystal structure of the haemagglutinin from a H10N7 seal influenza virus isolated in Germany in complex with avian receptor analogue, 3'-SLN | ||||||
![]() | (Hemagglutinin ...) x 2 | ||||||
![]() | VIRAL PROTEIN / receptor binding / fusion of virus membrane with host plasma membrane | ||||||
Function / homology | ![]() 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 / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, J. / Xiong, X. / Purkiss, A. / Walker, P. / Gamblin, S. / Skehel, J.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Hemagglutinin Traits Determine Transmission of Avian A/H10N7 Influenza Virus between Mammals. Authors: Herfst, S. / Zhang, J. / Richard, M. / McBride, R. / Lexmond, P. / Bestebroer, T.M. / Spronken, M.I.J. / de Meulder, D. / van den Brand, J.M. / Rosu, M.E. / Martin, S.R. / Gamblin, S.J. / ...Authors: Herfst, S. / Zhang, J. / Richard, M. / McBride, R. / Lexmond, P. / Bestebroer, T.M. / Spronken, M.I.J. / de Meulder, D. / van den Brand, J.M. / Rosu, M.E. / Martin, S.R. / Gamblin, S.J. / Xiong, X. / Peng, W. / Bodewes, R. / van der Vries, E. / Osterhaus, A.D.M.E. / Paulson, J.C. / Skehel, J.J. / Fouchier, R.A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 584.3 KB | Display | ![]() |
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PDB format | ![]() | 484.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tjwC ![]() 6tjyC ![]() 6tvaC ![]() 6tvbC ![]() 6tvcC ![]() 6tvfC ![]() 6tvrC ![]() 6tvsC ![]() 6tvtC ![]() 6twhC ![]() 6twiC ![]() 6twsC ![]() 6twvC ![]() 6txoC ![]() 6ty1C ![]() 4d00S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Hemagglutinin ... , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein | Mass: 35499.078 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 20313.389 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 4 types, 20 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine #4: 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 #5: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 158 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2%-4% PEG6000, 0.1M HEPES pH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→68.55 Å / Num. obs: 123642 / % possible obs: 99.1 % / Redundancy: 3 % / CC1/2: 0.994 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.7→2.75 Å / Num. unique obs: 6123 / CC1/2: 0.503 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D00 Resolution: 2.7→68.55 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.677 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 244.89 Å2 / Biso mean: 105.153 Å2 / Biso min: 43.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→68.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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