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Yorodumi- PDB-5vty: Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza viru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vty | |||||||||
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Title | Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin G225Q/L226A mutant in complex with 3'-SLN | |||||||||
Components | (Hemagglutinin ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN / Influenza A virus / hemagglutinin / mutant / receptor binding | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 Similarity search - Function | |||||||||
Biological species | Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | |||||||||
Authors | Wu, N.C. / Wilson, I.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell Host Microbe / Year: 2017 Title: Diversity of Functionally Permissive Sequences in the Receptor-Binding Site of Influenza Hemagglutinin. Authors: Wu, N.C. / Xie, J. / Zheng, T. / Nycholat, C.M. / Grande, G. / Paulson, J.C. / Lerner, R.A. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vty.cif.gz | 608.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vty.ent.gz | 505.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vty_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 5vty_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 5vty_validation.xml.gz | 58.8 KB | Display | |
Data in CIF | 5vty_validation.cif.gz | 84.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/5vty ftp://data.pdbj.org/pub/pdb/validation_reports/vt/5vty | HTTPS FTP |
-Related structure data
Related structure data | 5vtqC 5vtrC 5vtuC 5vtvC 5vtwC 5vtxC 5vtzC 5vu4C 4fnkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
-Hemagglutinin ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 35535.945 Da / Num. of mol.: 3 / Mutation: G225Q/L226A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2) Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7 #2: Protein | Mass: 20041.131 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2) Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7 |
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-Sugars , 6 types, 12 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 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: 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 #7: Polysaccharide | #8: Sugar | |
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-Non-polymers , 1 types, 619 molecules
#9: Water | ChemComp-HOH / |
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-Details
Has protein modification | 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: 2.95 Å3/Da / Density % sol: 58.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 38% 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0331 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0331 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→110.67 Å / Num. obs: 78249 / % possible obs: 98.4 % / Redundancy: 6.1 % / CC1/2: 1 / Rpim(I) all: 0.04 / Rsym value: 0.1 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7002 / CC1/2: 0.8 / Rpim(I) all: 0.26 / Rsym value: 0.54 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FNK Resolution: 2.36→110.67 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 12.862 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 53.067 Å2
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Refinement step | Cycle: 1 / Resolution: 2.36→110.67 Å
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Refine LS restraints |
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