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Yorodumi- PDB-3d9j: Snapshots of the RNA processing factor SCAF8 bound to different p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d9j | ||||||
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Title | Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II | ||||||
Components | RNA-binding protein 16 | ||||||
Keywords | TRANSCRIPTION / SCAF8 / RNA POLYMERASE II CTD INTERACTING DOMAIN / ARM REPEATS / PHOSPHO-CTD / Phosphoprotein / RNA-binding | ||||||
Function / homology | Function and homology information negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / RNA polymerase core enzyme binding / RNA polymerase II C-terminal domain phosphoserine binding / mRNA cleavage factor complex / positive regulation of DNA-templated transcription, elongation / termination of RNA polymerase II transcription / RNA polymerase II complex binding / nuclear matrix / mRNA binding / RNA binding ...negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled / RNA polymerase core enzyme binding / RNA polymerase II C-terminal domain phosphoserine binding / mRNA cleavage factor complex / positive regulation of DNA-templated transcription, elongation / termination of RNA polymerase II transcription / RNA polymerase II complex binding / nuclear matrix / mRNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Becker, R. / Loll, B. / Meinhart, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Snapshots of the RNA Processing Factor SCAF8 Bound to Different Phosphorylated Forms of the Carboxyl-terminal Domain of RNA Polymerase II. Authors: Becker, R. / Loll, B. / Meinhart, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d9j.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d9j.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 3d9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d9j_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 3d9j_full_validation.pdf.gz | 436.4 KB | Display | |
Data in XML | 3d9j_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 3d9j_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/3d9j ftp://data.pdbj.org/pub/pdb/validation_reports/d9/3d9j | HTTPS FTP |
-Related structure data
Related structure data | 3d9iSC 3d9kC 3d9lC 3d9mC 3d9nC 3d9oC 3d9pC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16940.648 Da / Num. of mol.: 2 Fragment: CTD INTERACTING DOMAIN OF SCAF8, UNP residues 1-136 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBM16, KIAA1116 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9UPN6 #2: Chemical | ChemComp-NH4 / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: 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: 2.62 Å3/Da / Density % sol: 53.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M citric acid, 2.8 M (NH4)2SO4, 1% (v/v) glycerol , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0007 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2006 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0007 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→41 Å / Num. obs: 44703 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 29.6 Å2 / Rsym value: 0.04 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 7158 / Rsym value: 0.271 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3D9I Resolution: 1.6→40.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.161 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.831 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→40.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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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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