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- PDB-5yki: Crystal structure of the engineered nine-repeat PUF domain in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yki | |||||||||
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Title | Crystal structure of the engineered nine-repeat PUF domain in complex with cognate 9nt-RNA | |||||||||
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![]() | RNA BINDING PROTEIN/RNA / PUF repeats / engineered protein / RNA recognition / RNA BINDING PROTEIN / 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 | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhao, Y.Y. / Wang, J. / Li, H.T. / Wang, Z.X. / Wu, J.W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Expanding RNA binding specificity and affinity of engineered PUF domains. Authors: Zhao, Y.Y. / Mao, M.W. / Zhang, W.J. / Wang, J. / Li, H.T. / Yang, Y. / Wang, Z. / Wu, J.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.2 KB | Display | ![]() |
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PDB format | ![]() | 73.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.8 KB | Display | ![]() |
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Full document | ![]() | 445.5 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ykhC ![]() 1m8zS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48061.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This is an engineered protein, which is made up of fragments of the RNA binding domain (PUF domain) of human Pumilio1 (Uniprot No. Q14671). Source: (gene. exp.) ![]() ![]() ![]() |
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#2: RNA chain | Mass: 2834.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 0.1M BIS-TRIS Propane, pH 8.8, 20% PEG MME 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2013 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91939 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 22954 / % possible obs: 99.6 % / Redundancy: 9.4 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1095 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1M8Z Resolution: 2.25→49 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→49 Å
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Refine LS restraints |
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LS refinement shell |
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