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Yorodumi- PDB-3erc: Crystal structure of the heterodimeric vaccinia virus mRNA polyad... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3erc | ||||||
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Title | Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATP | ||||||
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: 3.21 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 | 3erc.cif.gz | 293 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3erc.ent.gz | 236.1 KB | Display | PDB format |
PDBx/mmJSON format | 3erc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/3erc ftp://data.pdbj.org/pub/pdb/validation_reports/er/3erc | HTTPS FTP |
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-Related structure data
Related structure data | 3er8C 3er9C 2ga9S 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
-Protein , 2 types, 4 molecules ABCD
#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 |
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-RNA/DNA chimera (5'- ... , 3 types, 4 molecules EFGI
#3: RNA chain | Mass: 1434.920 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: RNA chain | | Mass: 1145.738 Da / Num. of mol.: 1 / Source method: obtained synthetically #5: RNA chain | | Mass: 1434.920 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 9 molecules
#6: Chemical | #7: Chemical | #8: Chemical | ChemComp-CA / #9: 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: 2.67 Å3/Da / Density % sol: 53.97 % | ||||||||||||||||||||||||||||||||||||||||
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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: BL7-1 / Wavelength: 0.9767 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2008 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9767 Å / Relative weight: 1 |
Reflection | Resolution: 3.21→50 Å / Num. obs: 30209 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 12.67 |
Reflection shell | Resolution: 3.21→3.41 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 1.93 / Rsym value: 0.427 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GA9 Resolution: 3.21→38.55 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 866011.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber 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: BULK FLAT MODEL / Bsol: 46.3876 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.21→38.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.21→3.41 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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