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Yorodumi- PDB-6ty1: Crystal structure of the haemagglutinin mutant (Gln226Leu, Gly228... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ty1 | ||||||
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Title | Crystal structure of the haemagglutinin mutant (Gln226Leu, Gly228Ser) from an H10N7 seal influenza virus isolated in Germany in complex with human receptor analogue 6'-SLN | ||||||
Components |
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Keywords | VIRAL PROTEIN / receptor binding / fusion of virus membrane with host plasma membrane | ||||||
Function / homology | Function and homology information 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 Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Zhang, J. / Xiong, X. / Purkiss, A. / Walker, P. / Gamblin, S. / Skehel, J.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Cell Host Microbe / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ty1.cif.gz | 572.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ty1.ent.gz | 473.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ty1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/6ty1 ftp://data.pdbj.org/pub/pdb/validation_reports/ty/6ty1 | HTTPS FTP |
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-Related structure data
Related structure data | 6tjwC 6tjyC 6tvaC 6tvbC 6tvcC 6tvdC 6tvfC 6tvrC 6tvsC 6tvtC 6twhC 6twiC 6twsC 6twvC 6txoC 4d00S 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein | Mass: 35514.137 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/harbour seal/Germany/1/2014(H10N7)) Gene: HA / Cell line (production host): Sf9 / Production host: unidentified baculovirus / References: UniProt: A0A0A7HR51 #2: Protein | Mass: 20313.389 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/harbour seal/Germany/1/2014(H10N7)) Gene: HA / Cell line (production host): Sf9 / Production host: unidentified baculovirus / References: UniProt: A0A0A7HR51 |
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-Sugars , 4 types, 13 molecules
#3: Polysaccharide | #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / #6: Sugar | |
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-Non-polymers , 1 types, 2 molecules
#7: Water | ChemComp-HOH / |
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-Details
Has ligand of interest | N |
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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: 3.4 Å3/Da / Density % sol: 63.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 6% PEG3350, 0.1 M MES pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→87.08 Å / Num. obs: 71930 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.997 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 3.2→3.28 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5351 / CC1/2: 0.663 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D00 Resolution: 3.2→87.08 Å / Cor.coef. Fo:Fc: 0.845 / Cor.coef. Fo:Fc free: 0.805 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.636 / 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: 295.77 Å2 / Biso mean: 121.0599 Å2 / Biso min: 45.49 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→87.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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