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Yorodumi- PDB-5vtu: Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza viru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vtu | |||||||||
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Title | Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin G225L/L226S mutant apo form | |||||||||
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: 2.45 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 | 5vtu.cif.gz | 594.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vtu.ent.gz | 494.1 KB | Display | PDB format |
PDBx/mmJSON format | 5vtu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vtu_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 5vtu_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 5vtu_validation.xml.gz | 53.8 KB | Display | |
Data in CIF | 5vtu_validation.cif.gz | 75 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/5vtu ftp://data.pdbj.org/pub/pdb/validation_reports/vt/5vtu | HTTPS FTP |
-Related structure data
Related structure data | 5vtqC 5vtrC 5vtvC 5vtwC 5vtxC 5vtyC 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: 35536.973 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 #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 , 5 types, 12 molecules
#3: 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 | ||||||
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#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 | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 274 molecules
#8: 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: 2.84 Å3/Da / Density % sol: 56.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium nitrate and 20% PEG 3350 |
-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: 2.45→50 Å / Num. obs: 66821 / % possible obs: 98 % / Redundancy: 6.3 % / CC1/2: 1 / Rpim(I) all: 0.04 / Rsym value: 0.1 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.45→2.53 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5155 / CC1/2: 0.81 / Rpim(I) all: 0.26 / Rsym value: 0.52 / % possible all: 83.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FNK Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 19.057 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.444 / ESU R Free: 0.241 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.35 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→50 Å
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Refine LS restraints |
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