[English] 日本語
![](img/lk-miru.gif)
- PDB-5t16: Crystal structure of yeast RNase III (Rnt1p) complexed with a non... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5t16 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of yeast RNase III (Rnt1p) complexed with a non-hydrolyzable RNA substrate analog | ||||||
![]() |
| ||||||
![]() | hydrolase/rna / Rnt1p / RNase III / substrate-loaded complex / hydrolase-rna complex | ||||||
Function / homology | ![]() box C/D sno(s)RNA processing / box H/ACA sno(s)RNA processing / regulation of fungal-type cell wall organization / termination of RNA polymerase II transcription, exosome-dependent / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / U4 snRNA 3'-end processing / ribonuclease III / apoptotic DNA fragmentation / deoxyribonuclease I activity ...box C/D sno(s)RNA processing / box H/ACA sno(s)RNA processing / regulation of fungal-type cell wall organization / termination of RNA polymerase II transcription, exosome-dependent / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / U4 snRNA 3'-end processing / ribonuclease III / apoptotic DNA fragmentation / deoxyribonuclease I activity / ribonuclease III activity / pre-miRNA processing / siRNA processing / RISC complex / termination of RNA polymerase II transcription / rRNA transcription / rRNA processing / double-stranded RNA binding / chromatin organization / nucleolus / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Song, H. / Ji, X. | ||||||
![]() | ![]() Title: The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III. Authors: Song, H. / Fang, X. / Jin, L. / Shaw, G.X. / Wang, Y.X. / Ji, X. #1: ![]() Title: Structure of a eukaryotic RNase III postcleavage complex reveals a double-ruler mechanism for substrate selection. Authors: Liang, Y.H. / Lavoie, M. / Comeau, M.A. / Abou Elela, S. / Ji, X. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 491.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 394.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 587.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 632.5 KB | Display | |
Data in XML | ![]() | 80.5 KB | Display | |
Data in CIF | ![]() | 112 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4oogS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 31481.312 Da / Num. of mol.: 4 / Fragment: unp residues 184-499 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RNT1, YMR239C, YM9408.01C, YM9959.21 / Production host: ![]() ![]() #2: Protein | Mass: 13975.908 Da / Num. of mol.: 8 / Fragment: unp residues 41-199 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RNT1, YMR239C, YM9408.01C, YM9959.21 / Production host: ![]() ![]() #3: RNA chain | Mass: 10940.617 Da / Num. of mol.: 4 / Source method: obtained synthetically #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.49 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M di ammonium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 6, 2015 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→38.99 Å / Num. obs: 86174 / % possible obs: 99.3 % / Redundancy: 4.5 % / Net I/σ(I): 6.79 |
Reflection shell | Resolution: 2.78→2.9 Å / Redundancy: 3.8 % / % possible all: 96 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4OOG Resolution: 2.783→38.985 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.92
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.783→38.985 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|