[English] 日本語
![](img/lk-miru.gif)
- PDB-5ygf: Crystal structure of Drosophila melanogaster Papi extended Tudor ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5ygf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Drosophila melanogaster Papi extended Tudor domain (D287A) in complex with Piwi N-terminal R10-unme peptide | ||||||
![]() |
| ||||||
![]() | PROTEIN BINDING / piRNA / complex / extended Tudor domain | ||||||
Function / homology | ![]() Yb body / piRNA-mediated heterochromatin formation / male germ-line stem cell asymmetric division / primary piRNA processing / germarium-derived oocyte fate determination / piRNA-mediated retrotransposon silencing by heterochromatin formation / retrotransposon silencing by heterochromatin formation / P granule organization / pole cell formation / piRNA binding ...Yb body / piRNA-mediated heterochromatin formation / male germ-line stem cell asymmetric division / primary piRNA processing / germarium-derived oocyte fate determination / piRNA-mediated retrotransposon silencing by heterochromatin formation / retrotransposon silencing by heterochromatin formation / P granule organization / pole cell formation / piRNA binding / female germ-line stem cell asymmetric division / post-transcriptional gene silencing / piRNA processing / positive regulation of DNA methylation-dependent heterochromatin formation / germ-line stem cell population maintenance / chromocenter / retrotransposon silencing / regulatory ncRNA-mediated gene silencing / P granule / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / germ cell nucleus / oogenesis / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / heterochromatin / heterochromatin formation / RNA endonuclease activity / P-body / euchromatin / chromatin DNA binding / spermatogenesis / chromatin / protein-containing complex / mitochondrion / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y.H. / Huang, Y. | ||||||
![]() | ![]() Title: Structural insights into the sequence-specific recognition of Piwi byDrosophilaPapi Authors: Zhang, Y. / Liu, W. / Li, R. / Gu, J. / Wu, P. / Peng, C. / Ma, J. / Wu, L. / Yu, Y. / Huang, Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 67 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 47.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 433 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ygbC ![]() 5ygcC ![]() 5ygdC ![]() 3fdrS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 25112.564 Da / Num. of mol.: 1 / Fragment: UNP residues 259-479 / Mutation: D287A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 1101.225 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.56 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M Sodium malonate pH 7.0, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97854 Å / Relative weight: 1 |
Reflection | Resolution: 1.698→30 Å / Num. obs: 29124 / % possible obs: 99.9 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 36.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.3 / % possible all: 99.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3FDR Resolution: 1.698→29.478 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 23.22
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.698→29.478 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|