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Yorodumi- PDB-8tj7: CRYSTAL STRUCTURE OF THE A/Shandong/9/1993(H3N2) INFLUENZA VIRUS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tj7 | |||||||||
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Title | CRYSTAL STRUCTURE OF THE A/Shandong/9/1993(H3N2) INFLUENZA VIRUS HEMAGGLUTININ WITH HUMAN RECEPTOR ANALOG 6'-SLNLN | |||||||||
Components | (Hemagglutinin ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / INFLUENZA / HEMAGGLUTININ / RECEPTOR | |||||||||
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: 2.85 Å | |||||||||
Authors | Wu, N.C. / Zhu, X. / Wilson, I.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell Host Microbe / Year: 2024 Title: Evolution of human H3N2 influenza virus receptor specificity has substantially expanded the receptor-binding domain site. Authors: Thompson, A.J. / Wu, N.C. / Canales, A. / Kikuchi, C. / Zhu, X. / de Toro, B.F. / Canada, F.J. / Worth, C. / Wang, S. / McBride, R. / Peng, W. / Nycholat, C.M. / Jimenez-Barbero, J. / ...Authors: Thompson, A.J. / Wu, N.C. / Canales, A. / Kikuchi, C. / Zhu, X. / de Toro, B.F. / Canada, F.J. / Worth, C. / Wang, S. / McBride, R. / Peng, W. / Nycholat, C.M. / Jimenez-Barbero, J. / Wilson, I.A. / Paulson, J.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tj7.cif.gz | 216.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tj7.ent.gz | 171.2 KB | Display | PDB format |
PDBx/mmJSON format | 8tj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/8tj7 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/8tj7 | HTTPS FTP |
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-Related structure data
Related structure data | 8tj4C 8tj6C 8tj8C 8tj9C 8tjaC 8tjbC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Hemagglutinin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 35759.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Shandong/9/1993(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B8K0N5 |
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#2: Protein | Mass: 20031.178 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Shandong/9/1993(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B8K0N5 |
-Sugars , 4 types, 8 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 | ||||
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#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #6: Sugar | |
-Non-polymers , 1 types, 19 molecules
#7: Water | ChemComp-HOH / |
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-Details
Has ligand of interest | Y |
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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: 4.52 Å3/Da / Density % sol: 72.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 40% PEG-400 and 0.1 M imidazole pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97741 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→33.25 Å / Num. obs: 22883 / % possible obs: 99.8 % / Redundancy: 3.9 % / CC1/2: 0.967 / Rpim(I) all: 0.04 / Rsym value: 0.17 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.85→2.95 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2316 / CC1/2: 0.7 / Rpim(I) all: 0.52 / Rsym value: 0.92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→33.25 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→33.25 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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