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Yorodumi- PDB-7s0i: CRYSTAL STRUCTURE OF N1 NEURAMINIDASE FROM A/Michigan/45/2015(H1N1) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s0i | ||||||||||||
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Title | CRYSTAL STRUCTURE OF N1 NEURAMINIDASE FROM A/Michigan/45/2015(H1N1) | ||||||||||||
Components | Neuraminidase | ||||||||||||
Keywords | HYDROLASE / Influenza A virus / H1N1 / neuraminidase / head domain / measles virus phosphoprotein tetramerization domain | ||||||||||||
Function / homology | Function and homology information exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Influenza A virus | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.892 Å | ||||||||||||
Authors | Zhu, X. / Wilson, I.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Mbio / Year: 2021 Title: A Novel Recombinant Influenza Virus Neuraminidase Vaccine Candidate Stabilized by a Measles Virus Phosphoprotein Tetramerization Domain Provides Robust Protection from Virus Challenge in the Mouse Model. Authors: Strohmeier, S. / Amanat, F. / Zhu, X. / McMahon, M. / Deming, M.E. / Pasetti, M.F. / Neuzil, K.M. / Wilson, I.A. / Krammer, F. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s0i.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s0i.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 7s0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s0i_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7s0i_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7s0i_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 7s0i_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/7s0i ftp://data.pdbj.org/pub/pdb/validation_reports/s0/7s0i | HTTPS FTP |
-Related structure data
Related structure data | 3nssS 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: 43264.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Michigan/45/2015(H1N1)) Strain: A/Michigan/45/2015(H1N1) / Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0X9QTS2, exo-alpha-sialidase | ||||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-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 | ||||
#3: Sugar | ChemComp-NAG / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M calcium acetate, 20% (w/v) polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2020 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.892→46.1 Å / Num. obs: 9713 / % possible obs: 91.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 59 Å2 / CC1/2: 0.953 / Rpim(I) all: 0.14 / Rsym value: 0.35 / Net I/σ(I): 4 |
Reflection shell | Resolution: 2.9→2.95 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 478 / CC1/2: 0.81 / Rpim(I) all: 0.36 / Rsym value: 0.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NSS Resolution: 2.892→46.066 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.37 / 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 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 125.27 Å2 / Biso mean: 35.3545 Å2 / Biso min: 19.82 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.892→46.066 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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