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- PDB-7z1k: Crystal structure of the SPOC domain of human SHARP (SPEN) in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z1k | ||||||
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Title | Crystal structure of the SPOC domain of human SHARP (SPEN) in complex with RNA polymerase II CTD heptapeptide phosphorylated on Ser5 | ||||||
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![]() | TRANSCRIPTION / human SHARP / SPOC domain / RNA polymerase II CTD heptapeptide | ||||||
Function / homology | ![]() RHOBTB1 GTPase cycle / positive regulation of neurogenesis / Notch signaling pathway / transcription repressor complex / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / mRNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II ...RHOBTB1 GTPase cycle / positive regulation of neurogenesis / Notch signaling pathway / transcription repressor complex / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / mRNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Appel, L. / Grishkovskaya, I. / Slade, D. / Djinovic-Carugo, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators. Authors: Appel, L.M. / Franke, V. / Benedum, J. / Grishkovskaya, I. / Strobl, X. / Polyansky, A. / Ammann, G. / Platzer, S. / Neudolt, A. / Wunder, A. / Walch, L. / Kaiser, S. / Zagrovic, B. / ...Authors: Appel, L.M. / Franke, V. / Benedum, J. / Grishkovskaya, I. / Strobl, X. / Polyansky, A. / Ammann, G. / Platzer, S. / Neudolt, A. / Wunder, A. / Walch, L. / Kaiser, S. / Zagrovic, B. / Djinovic-Carugo, K. / Akalin, A. / Slade, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.8 KB | Display | ![]() |
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PDB format | ![]() | 34.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.2 KB | Display | ![]() |
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Full document | ![]() | 438.5 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z27C ![]() 1ow1S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18730.729 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1721.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.79 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Potassium thiocyanate, 30% w/v PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→36.58 Å / Num. obs: 26393 / % possible obs: 98.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 26.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.55→1.58 Å / Num. unique obs: 1257 / CC1/2: 0.203 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OW1 Resolution: 1.55→35.23 Å / SU ML: 0.2547 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.6153 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→35.23 Å
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Refine LS restraints |
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LS refinement shell |
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