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- PDB-2ght: CTD-specific phosphatase Scp1 in complex with peptide from C-term... -
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Basic information
Entry | Database: PDB / ID: 2ght | ||||||
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Title | CTD-specific phosphatase Scp1 in complex with peptide from C-terminal domain of RNA polymerase II | ||||||
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![]() | HYDROLASE / protein-peptide complex / HAD superfamily | ||||||
Function / homology | ![]() RNA polymerase II CTD heptapeptide repeat phosphatase activity / microfibril binding / Abortive elongation of HIV-1 transcript in the absence of Tat / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / 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 / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / 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 / PIWI-interacting RNA (piRNA) biogenesis / protein-serine/threonine phosphatase / 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 / mRNA Splicing - Minor Pathway / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / 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 / protein dephosphorylation / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / negative regulation of protein phosphorylation / promoter-specific chromatin binding / TP53 Regulates Transcription of DNA Repair Genes / DNA-templated transcription termination / Transcriptional regulation by small RNAs / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / kinase binding / negative regulation of neurogenesis / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / 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 / hydrolase activity / 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 / magnesium ion binding / DNA binding / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / Noel, J.P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 94.3 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ghqSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() References: UniProt: Q9GZU7, protein-serine/threonine phosphatase #2: Protein/peptide | Mass: 904.813 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.16 % |
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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) 2M 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2005 / Details: mirror |
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: 1.8→39.2 Å / Num. obs: 50244 / % possible obs: 90.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Rsym value: 0.04 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Mean I/σ(I) obs: 3 / Num. unique all: 7853 / Rsym value: 0.311 / % possible all: 77.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GHQ Resolution: 1.8→39.2 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 0.105 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→39.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018
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