+Open data
-Basic information
Entry | Database: PDB / ID: 4pz8 | ||||||
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Title | PCE1 guanylyltransferase bound to SPT5 CTD | ||||||
Components |
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Keywords | TRANSFERASE/TRANSCRIPTION / Nucleotidyl transferase / RNA capping enzyme / RNA polymerase II / Spt5 / guanylation / nuclear / TRANSFERASE-TRANSCRIPTION complex | ||||||
Function / homology | Function and homology information 7-methylguanosine RNA capping / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / negative regulation of antisense RNA transcription / mRNA capping enzyme complex / DSIF complex ...7-methylguanosine RNA capping / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / negative regulation of antisense RNA transcription / mRNA capping enzyme complex / DSIF complex / chromatin => GO:0000785 / transcription elongation factor activity / 7-methylguanosine mRNA capping / RNA polymerase II C-terminal domain binding / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / mRNA processing / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA binding / GTP binding / regulation of transcription by RNA polymerase II / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Doamekpor, S.K. / Lima, C.D. | ||||||
Citation | Journal: Genes Dev. / Year: 2014 Title: How an mRNA capping enzyme reads distinct RNA polymerase II and Spt5 CTD phosphorylation codes. Authors: Doamekpor, S.K. / Sanchez, A.M. / Schwer, B. / Shuman, S. / Lima, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pz8.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pz8.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 4pz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/4pz8 ftp://data.pdbj.org/pub/pdb/validation_reports/pz/4pz8 | HTTPS FTP |
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-Related structure data
Related structure data | 4pz6SC 4pz7C 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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Unit cell |
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-Components
#1: Protein | Mass: 47378.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Strain: 972 / ATCC 24843 / Gene: ceg1, ceg1/pce1, pce1, SPBC2F12.08c / Plasmid: pSMT3 (SUMO) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CP-RIL / References: UniProt: P40997, mRNA guanylyltransferase | ||
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#2: Protein/peptide | Mass: 1906.022 Da / Num. of mol.: 1 / Fragment: Spt5 C-terminal domain peptide / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13936*PLUS | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 61.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.35 M lithium sulfate, 0.5 M ammonium sulfate, 0.1 M sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2010 |
Radiation | Monochromator: Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 11807 / Num. obs: 11169 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.8 / Num. unique all: 950 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4PZ6 Resolution: 3.1→38.458 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 24.33 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→38.458 Å
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Refine LS restraints |
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LS refinement shell |
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