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Yorodumi- PDB-2ghq: CTD-specific phosphatase Scp1 in complex with peptide C-terminal ... -
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-Basic information
Entry | Database: PDB / ID: 2ghq | ||||||
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Title | CTD-specific phosphatase Scp1 in complex with peptide C-terminal domain of RNA polymerase II | ||||||
Components |
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Keywords | HYDROLASE / protein-peptide complex / HAD superfamily | ||||||
Function / homology | Function and homology information RNA polymerase II CTD heptapeptide repeat phosphatase activity / microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / myosin phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection ...RNA polymerase II CTD heptapeptide repeat phosphatase activity / microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / myosin phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / protein-serine/threonine phosphatase / PIWI-interacting RNA (piRNA) biogenesis / mRNA Splicing - Minor Pathway / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II activity / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of neuron differentiation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / mRNA Splicing - Major Pathway / protein dephosphorylation / positive regulation of RNA splicing / negative regulation of protein phosphorylation / promoter-specific chromatin binding / DNA-templated transcription termination / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation by small RNAs / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / kinase binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / negative regulation of neurogenesis / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / Estrogen-dependent gene expression / transcription by RNA polymerase II / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Zhang, Y. / Noel, J.P. | ||||||
Citation | Journal: Mol.Cell / Year: 2006 Title: Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1. Authors: Zhang, Y. / Kim, Y. / Genoud, N. / Gao, J. / Kelly, J.W. / Pfaff, S.L. / Gill, G.N. / Dixon, J.E. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ghq.cif.gz | 91 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ghq.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ghq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/2ghq ftp://data.pdbj.org/pub/pdb/validation_reports/gh/2ghq | HTTPS FTP |
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-Related structure data
Related structure data | 2ghtC 1ta0S 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: 20876.754 Da / Num. of mol.: 2 / Mutation: D96N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTDSP1 / Plasmid: pet28 derivatives / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9GZU7, protein-serine/threonine phosphatase #2: Protein/peptide | Mass: 1081.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P24928, DNA-directed RNA polymerase #3: Chemical | #4: 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: 3.23 Å3/Da / Density % sol: 61.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: (1)0.5M Ammonium sulfate, 0.2M Lithium sulfate, 100mM HEPES 7.5 (2) 1M sodium tartrate, 100mM Tris pH 8.5 , pH 7.5 - 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2005 / 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: 2.04→48.98 Å / Num. obs: 35704 / % possible obs: 95.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Rsym value: 0.079 / Net I/σ(I): 11.94 |
Reflection shell | Resolution: 2.04→2.14 Å / Mean I/σ(I) obs: 2.79 / Num. unique all: 4865 / Rsym value: 0.48 / % possible all: 76.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1ta0 Resolution: 2.05→48.98 Å / Isotropic thermal model: isotropic / Cross valid method: throughtout / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: -0.397 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→48.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.02
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