+Open data
-Basic information
Entry | Database: PDB / ID: 6npw | ||||||
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Title | SSu72/Sympk in complex with Ser2/Ser5 phosphorylated peptide | ||||||
Components |
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Keywords | HYDROLASE / phosphatase / CTD of RNA pol II | ||||||
Function / homology | Function and homology information Processing of Intronless Pre-mRNAs / histone locus body / Processing of Capped Intron-Containing Pre-mRNA / mRNA 3'-end processing / tricellular tight junction / RNA Polymerase II Transcription Termination / RNA polymerase II transcribes snRNA genes / Transport of Mature mRNA Derived from an Intronless Transcript / RNA polymerase II CTD heptapeptide repeat phosphatase activity / mRNA 3'-end processing by stem-loop binding and cleavage ...Processing of Intronless Pre-mRNAs / histone locus body / Processing of Capped Intron-Containing Pre-mRNA / mRNA 3'-end processing / tricellular tight junction / RNA Polymerase II Transcription Termination / RNA polymerase II transcribes snRNA genes / Transport of Mature mRNA Derived from an Intronless Transcript / RNA polymerase II CTD heptapeptide repeat phosphatase activity / mRNA 3'-end processing by stem-loop binding and cleavage / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / Processing of Capped Intron-Containing Pre-mRNA / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / myosin phosphatase activity / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / protein-serine/threonine phosphatase / Formation of TC-NER Pre-Incision Complex / phosphatase activity / Gap-filling DNA repair synthesis and ligation in TC-NER / Estrogen-dependent gene expression / Dual incision in TC-NER / RNA polymerase II, core complex / translesion synthesis / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) Saccharomyces cerevisiae RM11-1a (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.486 Å | ||||||
Authors | Irani, S. / Zhang, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Structural determinants for accurate dephosphorylation of RNA polymerase II by its cognate C-terminal domain (CTD) phosphatase during eukaryotic transcription. Authors: Irani, S. / Sipe, S.N. / Yang, W. / Burkholder, N.T. / Lin, B. / Sim, K. / Matthews, W.L. / Brodbelt, J.S. / Zhang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6npw.cif.gz | 220.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6npw.ent.gz | 174 KB | Display | PDB format |
PDBx/mmJSON format | 6npw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6npw_validation.pdf.gz | 480.9 KB | Display | wwPDB validaton report |
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Full document | 6npw_full_validation.pdf.gz | 493.8 KB | Display | |
Data in XML | 6npw_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 6npw_validation.cif.gz | 54.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/6npw ftp://data.pdbj.org/pub/pdb/validation_reports/np/6npw | HTTPS FTP |
-Related structure data
Related structure data | 4imiS S: Starting model for refinement |
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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: 37495.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sym, CG2097 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q8MSU4 #2: Protein | Mass: 23130.279 Da / Num. of mol.: 2 / Mutation: C13D, D144N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ssu72, CG14216, Dmel_CG14216 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: Q9VWE4, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, protein-serine/threonine phosphatase, EC: 3.1.3.41 #3: Protein/peptide | | Mass: 2138.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae RM11-1a (yeast) / References: UniProt: P04050*PLUS #4: Chemical | ChemComp-PO4 / | #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: 3.5 Å3/Da / Density % sol: 64.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 12% PEG3350 (w/v) and 100 mM HEPE pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.486→50 Å / Num. obs: 59967 / % possible obs: 100 % / Redundancy: 5 % / Net I/σ(I): 11.97 |
Reflection shell | Resolution: 2.49→2.55 Å / Num. unique obs: 4110 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IMI Resolution: 2.486→48.943 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.486→48.943 Å
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Refine LS restraints |
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LS refinement shell |
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