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Yorodumi- PDB-6ns9: Crystal structure of the IVR-165 (H3N2) influenza virus hemagglut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ns9 | |||||||||
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Title | Crystal structure of the IVR-165 (H3N2) influenza virus hemagglutinin apo form | |||||||||
Components | (Hemagglutinin ...) x 2 | |||||||||
Keywords | VIRAL PROTEIN | |||||||||
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: 1.95 Å | |||||||||
Authors | Wu, N.C. / Wilson, I.A. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Cell Host Microbe / Year: 2019 Title: Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Authors: Wu, N.C. / Lv, H. / Thompson, A.J. / Wu, D.C. / Ng, W.W.S. / Kadam, R.U. / Lin, C.W. / Nycholat, C.M. / McBride, R. / Liang, W. / Paulson, J.C. / Mok, C.K.P. / 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 | 6ns9.cif.gz | 229.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ns9.ent.gz | 184 KB | Display | PDB format |
PDBx/mmJSON format | 6ns9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ns9_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6ns9_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6ns9_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 6ns9_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/6ns9 ftp://data.pdbj.org/pub/pdb/validation_reports/ns/6ns9 | HTTPS FTP |
-Related structure data
Related structure data | 6nsaC 6nsbC 6nscC 6nsfC 6nsgC 4o5nS 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 on special symmetry positions |
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-Components
-Hemagglutinin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 35856.465 Da / Num. of mol.: 1 / Fragment: residues 27-345 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: L0HR89 |
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#2: Protein | Mass: 20153.393 Da / Num. of mol.: 1 / Fragment: residues 346-521 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: L0HR89 |
-Sugars , 4 types, 8 molecules
#3: 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 | ||||
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#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: 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 #6: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 406 molecules
#7: Water | ChemComp-HOH / |
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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: 3.31 Å3/Da / Density % sol: 62.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 44% 2-methyl-2,4-pentanediol, 0.1 M HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 54947 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 25 Å2 / CC1/2: 1 / Rpim(I) all: 0.04 / Rsym value: 0.15 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.95→2.01 Å / Redundancy: 17.4 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4957 / CC1/2: 0.92 / Rpim(I) all: 0.22 / Rsym value: 0.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O5N Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.136 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.114 / 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: 44.227 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→50 Å
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Refine LS restraints |
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