+Open data
-Basic information
Entry | Database: PDB / ID: 7ruo | ||||||
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Title | Crystal structure of human UTP15 | ||||||
Components | U3 small nucleolar RNA-associated protein 15 homolog | ||||||
Keywords | RNA BINDING PROTEIN / WD-repeat / WDR / UTP15 / SGC / Structural Genomics / Structural Genomics Consortium | ||||||
Function / homology | Function and homology information positive regulation of rRNA processing / rRNA modification in the nucleus and cytosol / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / small-subunit processome / fibrillar center / rRNA processing / ribosomal small subunit biogenesis / nucleolus / endoplasmic reticulum ...positive regulation of rRNA processing / rRNA modification in the nucleus and cytosol / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / small-subunit processome / fibrillar center / rRNA processing / ribosomal small subunit biogenesis / nucleolus / endoplasmic reticulum / RNA binding / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Dehghani-Tafti, S. / Dong, A. / Zeng, H. / Hutchinson, A. / Seitova, A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: Crystal structure of human UTP15 Authors: Dehghani-Tafti, S. / Dong, A. / Zeng, H. / Hutchinson, A. / Seitova, A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ruo.cif.gz | 137.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ruo.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ruo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ruo_validation.pdf.gz | 445.1 KB | Display | wwPDB validaton report |
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Full document | 7ruo_full_validation.pdf.gz | 449.2 KB | Display | |
Data in XML | 7ruo_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 7ruo_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/7ruo ftp://data.pdbj.org/pub/pdb/validation_reports/ru/7ruo | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-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: 43938.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UTP15 / Plasmid: pFBOH-MHL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TED0 #2: Chemical | ChemComp-UNX / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 1.94 Å3/Da / Density % sol: 36.45 % / Mosaicity: 0.26 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.0M (NH4)2SO4, 0.2M Sodium acetate, 0.1M Hepes pH7.5, 5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: May 4, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→55.47 Å / Num. obs: 57233 / % possible obs: 93.7 % / Redundancy: 2.2 % / CC1/2: 0.982 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.096 / Rrim(I) all: 0.145 / Net I/σ(I): 4.7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.69 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.686 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 58.16 Å2 / Biso mean: 14.976 Å2 / Biso min: 6.16 Å2
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Refinement step | Cycle: final / Resolution: 1.8→42.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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