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Yorodumi- PDB-6gol: Three dimensional structure of a novel influenza hemagglutinin tr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gol | ||||||
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Title | Three dimensional structure of a novel influenza hemagglutinin tri-stalk protein | ||||||
Components | Hemagglutinin tri-stalk | ||||||
Keywords | VIRAL PROTEIN / Hemagglutinin stem / Long alpha helix / Influenza / Post-fusion conformation / Tri-stalk protein | ||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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: 1.7 Å | ||||||
Authors | Kirsteina, A. / Kazaks, A. / Tars, K. | ||||||
Funding support | Latvia, 1items
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Citation | Journal: PLoS ONE / Year: 2018 Title: Structure and applications of novel influenza HA tri-stalk protein for evaluation of HA stem-specific immunity. Authors: Lu, I.N. / Kirsteina, A. / Farinelle, S. / Willieme, S. / Tars, K. / Muller, C.P. / Kazaks, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gol.cif.gz | 27.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gol.ent.gz | 17 KB | Display | PDB format |
PDBx/mmJSON format | 6gol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/6gol ftp://data.pdbj.org/pub/pdb/validation_reports/go/6gol | HTTPS FTP |
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-Related structure data
Related structure data | 1htmS S: Starting model for refinement |
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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
#1: Protein | Mass: 8554.573 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/California/VRDL69/2009(H1N1)) Production host: Escherichia coli (E. coli) / References: UniProt: D3G5J5 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2.0 M ammonium sulfate and 0.1 M Bis-Tris, pH 5.5, protein 10 mg/mL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2015 / Details: RH-COATED TOROIDAL SI MIRROR |
Radiation | Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→23.12 Å / Num. obs: 9803 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1439 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HTM Resolution: 1.7→23.12 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.352 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.096 / 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: 36.711 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→23.12 Å
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Refine LS restraints |
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