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Yorodumi- PDB-3q0m: Crystal structure of the PUMILIO-homology domain from Human PUMIL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q0m | ||||||
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Title | Crystal structure of the PUMILIO-homology domain from Human PUMILIO1 in complex with p38alpha NREb | ||||||
Components |
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Keywords | RNA binding protein/RNA / PUF / PUMILIO-homolgy domain / Gene regulation / RNA binding / RNA binding protein-RNA complex | ||||||
Function / homology | Function and homology information regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / regulation of chromosome segregation / positive regulation of RIG-I signaling pathway / post-transcriptional gene silencing / 3'-UTR-mediated mRNA destabilization / miRNA processing / miRNA binding / post-transcriptional regulation of gene expression / Golgi Associated Vesicle Biogenesis ...regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / regulation of chromosome segregation / positive regulation of RIG-I signaling pathway / post-transcriptional gene silencing / 3'-UTR-mediated mRNA destabilization / miRNA processing / miRNA binding / post-transcriptional regulation of gene expression / Golgi Associated Vesicle Biogenesis / mRNA destabilization / regulation of mRNA stability / adult locomotory behavior / mRNA 3'-UTR binding / stem cell differentiation / P-body / cytoplasmic stress granule / regulation of translation / spermatogenesis / regulation of cell cycle / axon / RNA binding / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.705 Å | ||||||
Authors | Lu, G. / Hall, T.M.T. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Alternate modes of cognate RNA recognition by human PUMILIO proteins. Authors: Lu, G. / Hall, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q0m.cif.gz | 154.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q0m.ent.gz | 121.4 KB | Display | PDB format |
PDBx/mmJSON format | 3q0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/3q0m ftp://data.pdbj.org/pub/pdb/validation_reports/q0/3q0m | HTTPS FTP |
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-Related structure data
Related structure data | 3q0lC 3q0nC 3q0oC 3q0pC 3q0qC 3q0rC 3q0sC C: citing same article (ref.) |
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Similar structure data |
-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: 40364.523 Da / Num. of mol.: 2 / Fragment: UNP residues 828-1176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PUM1, KIAA0099, PUMH1 / Plasmid: pTYB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14671 #2: RNA chain | Mass: 2551.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This RNA sequence occurs naturally in humans. #3: 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: 2.08 Å3/Da / Density % sol: 40.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 15-20% (w/v) PEG 3350, 100 mM Li2SO4, and 100 mM Na3Citrate pH 5.5-6.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Mar 25, 2009 |
Radiation | Monochromator: varimax hf / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29.8 Å / Num. all: 20640 / Num. obs: 16244 / % possible obs: 78.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.7→2.8 Å / % possible all: 80.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.705→29.8 Å / SU ML: 1.78 / σ(F): 0.07 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.997 Å2 / ksol: 0.323 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.705→29.8 Å
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Refine LS restraints |
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LS refinement shell |
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