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Yorodumi- PDB-6e7h: Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Na... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e7h | |||||||||
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Title | Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1 influenza virus in complex with 3'-GcLN | |||||||||
Components | (Hemagglutinin ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / Influenza virus / hemagglutinin / HA / H5N1 / A/Viet Nam/1203/2004 / Receptor specificity | |||||||||
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 ...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 / membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Tzarum, N. / Wilson, I.A. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Cell Rep / Year: 2019 Title: N-Glycolylneuraminic Acid as a Receptor for Influenza A Viruses. Authors: Broszeit, F. / Tzarum, N. / Zhu, X. / Nemanichvili, N. / Eggink, D. / Leenders, T. / Li, Z. / Liu, L. / Wolfert, M.A. / Papanikolaou, A. / Martinez-Romero, C. / Gagarinov, I.A. / Yu, W. / ...Authors: Broszeit, F. / Tzarum, N. / Zhu, X. / Nemanichvili, N. / Eggink, D. / Leenders, T. / Li, Z. / Liu, L. / Wolfert, M.A. / Papanikolaou, A. / Martinez-Romero, C. / Gagarinov, I.A. / Yu, W. / Garcia-Sastre, A. / Wennekes, T. / Okamatsu, M. / Verheije, M.H. / Wilson, I.A. / Boons, G.J. / de Vries, R.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e7h.cif.gz | 289.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e7h.ent.gz | 232.3 KB | Display | PDB format |
PDBx/mmJSON format | 6e7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/6e7h ftp://data.pdbj.org/pub/pdb/validation_reports/e7/6e7h | HTTPS FTP |
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-Related structure data
Related structure data | 6e7gSC 6n5aC 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
-Hemagglutinin ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 37855.922 Da / Num. of mol.: 3 / Mutation: Y161A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1)) Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5EP31, UniProt: Q6DQ33*PLUS #2: Protein | Mass: 20414.504 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1)) Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6DQ18 |
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-Sugars , 4 types, 6 molecules
#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 | N-glycolyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | |
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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: 3.11 Å3/Da / Density % sol: 60.48 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% (w/v) PEG 3350, 0.1M Na-Acetate, pH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 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: 3.3→50 Å / Num. obs: 31184 / % possible obs: 97.3 % / Redundancy: 3.5 % / CC1/2: 0.92 / Rpim(I) all: 0.047 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 3.3→3.36 Å / Num. unique all: 15587 / CC1/2: 0.62 / Rpim(I) all: 0.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6E7G Resolution: 3.3→47.067 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→47.067 Å
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Refine LS restraints |
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LS refinement shell |
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