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Yorodumi- PDB-4p6q: The crystal structure of the Split End protein SHARP adds a new l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p6q | |||||||||
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Title | The crystal structure of the Split End protein SHARP adds a new layer of complexity to proteins containing RNA Recognition Motifs | |||||||||
Components | Msx2-interacting protein | |||||||||
Keywords | TRANSCRIPTION / RNA-recognition Motif / SPEN protein / Steroid RNA Activator / Transcriptional Regulation | |||||||||
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 / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Arieti, F. / Gabus, C. / Tambalo, M. / Huet, T. / Round, A. / Thore, S. | |||||||||
Funding support | Switzerland, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: The crystal structure of the Split End protein SHARP adds a new layer of complexity to proteins containing RNA recognition motifs. Authors: Arieti, F. / Gabus, C. / Tambalo, M. / Huet, T. / Round, A. / Thore, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p6q.cif.gz | 137.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p6q.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 4p6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p6q_validation.pdf.gz | 437.4 KB | Display | wwPDB validaton report |
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Full document | 4p6q_full_validation.pdf.gz | 438.9 KB | Display | |
Data in XML | 4p6q_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 4p6q_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/4p6q ftp://data.pdbj.org/pub/pdb/validation_reports/p6/4p6q | HTTPS FTP |
-Related structure data
Related structure data | 1whyS 1x55S 2adcS 2cpeS 2cpzS 2cqbS 2dguS 2dnmS 2i38S 2lcwS 2ytcS 3md1S 4f26S 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: 33056.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPEN, KIAA0929, MINT, SHARP / Plasmid: pET42a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q96T58 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 15% PEG 8000, 0.1M ammonium sulphate, 0.01M magnesium chloride, 0.05M 2-(N-morpholino)ethanesulfonic acid PH range: 5.4-6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.71 Å / Num. obs: 26164 / % possible obs: 99.67 % / Redundancy: 5.38 % / Net I/σ(I): 20.44 |
Reflection shell | Highest resolution: 2 Å / Redundancy: 5.63 % / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE). ...Starting model: Ensemble 1 (PDB codes: 3MD1, 2ADC, 2DNM, 2DGU, 2CQB); Ensemble 2 (PDB codes: X4AR, 2YTC, 4F26, 1WHY, 2CPZ); Ensemble 3 (PDB codes: 2I38, 1WHY, 1X55, 2LCW, 2CPE). Resolution: 2→28.71 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 25.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.71 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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