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Yorodumi- PDB-3er8: Crystal structure of the heterodimeric vaccinia virus mRNA polyad... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3er8 | ||||||
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Title | Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with two fragments of RNA | ||||||
Components |
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Keywords | Transcription / Transferase/DNA / RNA / Polyadenylate polymerase / translocation / single tranded RNA poly(A) polymerase / RNA protein complex / processivity / heterodimer / nucleotidyltransferase / poxvirus / Methyltransferase / mRNA capping / mRNA processing / S-adenosyl-L-methionine / Transferase / RNA COMPLEX / Transferase-DNA | ||||||
Function / homology | Function and homology information regulation of mRNA 3'-end processing / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / 7-methylguanosine mRNA capping / translation elongation factor activity / virion component / mRNA processing / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / RNA binding ...regulation of mRNA 3'-end processing / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / 7-methylguanosine mRNA capping / translation elongation factor activity / virion component / mRNA processing / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | vaccinia virus WR | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å | ||||||
Authors | Li, C. / Li, H. / Zhou, S. / Poulos, T.L. / Gershon, P.D. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Polymerase Translocation with Respect to Single-Stranded Nucleic Acid: Looping or Wrapping of Primer around a Poly(A) Polymerase Authors: Li, C. / Li, H. / Zhou, S. / Sun, E. / Yoshizawa, J. / Poulos, T.L. / Gershon, P.D. #1: Journal: Mol.Cell / Year: 2006 Title: Crystal structure of the vaccinia virus polyadenylate polymerase heterodimer: insight into ATP selecttivity and processivity Authors: Moure, C.M. / Bowman, B.R. / Gershon, P.D. / Quiocho, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3er8.cif.gz | 282.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3er8.ent.gz | 229.9 KB | Display | PDB format |
PDBx/mmJSON format | 3er8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3er8_validation.pdf.gz | 479.8 KB | Display | wwPDB validaton report |
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Full document | 3er8_full_validation.pdf.gz | 575.2 KB | Display | |
Data in XML | 3er8_validation.xml.gz | 62.9 KB | Display | |
Data in CIF | 3er8_validation.cif.gz | 85.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/3er8 ftp://data.pdbj.org/pub/pdb/validation_reports/er/3er8 | HTTPS FTP |
-Related 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: 34588.961 Da / Num. of mol.: 2 / Mutation: R140A,K142A,R143A Source method: isolated from a genetically manipulated source Source: (gene. exp.) vaccinia virus WR / Strain: Western Reserve / WR / Gene: PAPS, VACWR095, F9 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLyS / References: UniProt: P07617, methyltransferase cap1 #2: Protein | Mass: 55574.125 Da / Num. of mol.: 2 / Mutation: L36S Source method: isolated from a genetically manipulated source Source: (gene. exp.) vaccinia virus WR / Strain: Western Reserve / WR / Gene: PAPL, VACWR057, E1L / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLyS References: UniProt: P23371, polynucleotide adenylyltransferase #3: DNA/RNA hybrid | | Mass: 1434.920 Da / Num. of mol.: 1 / Source method: obtained synthetically #4: DNA/RNA hybrid | | Mass: 856.556 Da / Num. of mol.: 1 / Source method: obtained synthetically #5: DNA/RNA hybrid | Mass: 856.556 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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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: 2.69 Å3/Da / Density % sol: 54.25 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.7 Details: proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. room ...Details: proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2007 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.18→50 Å / Num. obs: 30650 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 3.18→3.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2 / Rsym value: 0.526 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.18→38.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 603426.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: Residues 27-32, 142-144 in chains A & B and residues 1-11, 118-129, 150-160 in chains C & D are disordered and not included in the model.
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Solvent computation | Solvent model: FLAT MODEL, BULK FLAT MODEL / Bsol: 49.8436 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.18→38.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.18→3.38 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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