[English] 日本語
Yorodumi- PDB-7z1k: Crystal structure of the SPOC domain of human SHARP (SPEN) in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z1k | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the SPOC domain of human SHARP (SPEN) in complex with RNA polymerase II CTD heptapeptide phosphorylated on Ser5 | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / human SHARP / SPOC domain / RNA polymerase II CTD heptapeptide | ||||||
Function / homology | Function and homology information 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 / mRNA binding / negative regulation of DNA-templated transcription / 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 / mRNA binding / negative regulation of DNA-templated transcription / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Appel, L. / Grishkovskaya, I. / Slade, D. / Djinovic-Carugo, K. | ||||||
Funding support | Austria, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2023 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7z1k.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7z1k.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 7z1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/7z1k ftp://data.pdbj.org/pub/pdb/validation_reports/z1/7z1k | HTTPS FTP |
---|
-Related structure data
Related structure data | 7z27C 1ow1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18730.729 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPEN, KIAA0929, MINT, SHARP / Production host: Escherichia coli (E. coli) / References: UniProt: Q96T58 |
---|---|
#2: Protein/peptide | Mass: 1721.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.79 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|