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Yorodumi- PDB-3a1g: High-Resolution Crystal Structure of RNA polymerase PB1-PB2 subun... -
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-Basic information
Entry | Database: PDB / ID: 3a1g | ||||||
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Title | High-Resolution Crystal Structure of RNA polymerase PB1-PB2 subunits from Influenza A Virus | ||||||
Components |
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Keywords | TRANSFERASE / Influenza virus / RNA polymerase / Nucleotide-binding / Nucleotidyltransferase / Nucleus / RNA replication / RNA-directed RNA polymerase / Mitochondrion / mRNA capping / mRNA processing / Virion | ||||||
Function / homology | Function and homology information cRNA Synthesis / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis ...cRNA Synthesis / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Viral Messenger RNA Synthesis / vRNP Assembly / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / viral transcription / host cell mitochondrion / Viral mRNA Translation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / host cell cytoplasm / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Sugiyama, K. / Park, S.-Y. / Obayashi, E. | ||||||
Citation | Journal: Embo J. / Year: 2009 Title: Structural insight into the essential PB1-PB2 subunit contact of the influenza virus RNA polymerase Authors: Sugiyama, K. / Obayashi, E. / Kawaguchi, A. / Suzuki, Y. / Tame, J.R.H. / Nagata, K. / Park, S.-Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a1g.cif.gz | 59.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a1g.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 3a1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/3a1g ftp://data.pdbj.org/pub/pdb/validation_reports/a1/3a1g | HTTPS FTP |
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-Related structure data
Related structure data | 2zttSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 9675.504 Da / Num. of mol.: 2 / Fragment: PB1 C-terminal fragment, UNP residues 678-757 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/34(H1N1)) Strain: strain A/Puerto Rico/8/1934 H1N1 / Gene: PB1 / Plasmid: modified pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RILcodonPlus / References: UniProt: P03431, RNA-directed RNA polymerase #2: Protein/peptide | Mass: 4731.061 Da / Num. of mol.: 2 / Fragment: PB2 N-terminal ragment, UNP residues 1-37 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/34(H1N1)) Strain: strain A/Puerto Rico/8/1934 H1N1 / Gene: PB2 / Plasmid: midified pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RILcodonPlus / References: UniProt: P03428 #3: 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: 2.24 Å3/Da / Density % sol: 45.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 80mM Sodium Citrate, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 19, 2009 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 25865 / Num. obs: 25865 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 0 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 25 / % possible all: 73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZTT Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 2.709 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.543 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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