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- PDB-3q0m: Crystal structure of the PUMILIO-homology domain from Human PUMIL... -
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Open data
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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 | ||||||
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![]() | RNA binding protein/RNA / PUF / PUMILIO-homolgy domain / Gene regulation / RNA binding / RNA binding protein-RNA complex | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lu, G. / Hall, T.M.T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.7 KB | Display | ![]() |
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PDB format | ![]() | 121.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.8 KB | Display | ![]() |
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Full document | ![]() | 503.4 KB | Display | |
Data in XML | ![]() | 30.3 KB | Display | |
Data in CIF | ![]() | 42.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3q0lC ![]() 3q0nC ![]() 3q0oC ![]() 3q0pC ![]() 3q0qC ![]() 3q0rC ![]() 3q0sC C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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