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Yorodumi- PDB-3m8a: Crystal Structure of Swine Flu Virus NS1 N-Terminal RNA Binding D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m8a | ||||||
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Title | Crystal Structure of Swine Flu Virus NS1 N-Terminal RNA Binding Domain from H1N1 Influenza A/California/07/2009 | ||||||
Components | Nonstructural protein 1 | ||||||
Keywords | VIRAL PROTEIN / NS1 / N-terminal RNA binding Domain / Influenza A virus / H1N1 / Host cytoplasm / Host nucleus / Host-virus interaction / Interferon antiviral system evasion / RNA-binding / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Swine Flu Virus NS1 N-Terminal RNA Binding Domain from H1N1 Influenza A/California/07/2009 Authors: Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m8a.cif.gz | 209.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m8a.ent.gz | 169.3 KB | Display | PDB format |
PDBx/mmJSON format | 3m8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/3m8a ftp://data.pdbj.org/pub/pdb/validation_reports/m8/3m8a | HTTPS FTP |
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-Related structure data
Related structure data | 2z0aS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
-Components
#1: Protein | Mass: 8653.802 Da / Num. of mol.: 12 / Fragment: N-terminal RNA Binding Domain (UNP residues 1-73) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/CALIFORNIA/07/2009(H1N1) / References: UniProt: C3W611 #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-MLI / #4: Chemical | ChemComp-NA / #5: 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: 3.19 Å3/Da / Density % sol: 61.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Tacsimate 35%, ph 7, KCl 0.1M, MgCl2 0.1M, 0.3M NDSB211, TCEP 2mM, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 4, 2010 / Details: Be Lenes |
Radiation | Monochromator: Single Crystal Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 75867 / Num. obs: 75867 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 28.36 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z0A Resolution: 2.1→29.25 Å / Cor.coef. Fo:Fc: 0.9429 / Cor.coef. Fo:Fc free: 0.9229 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.216 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→29.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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