[English] 日本語
![](img/lk-miru.gif)
- PDB-4nh5: Structure of human Dicer Platform-PAZ-Connector Helix cassette in... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4nh5 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 14-mer siRNA having 5'-pUU and UU-3' ends (2.55 Angstrom resolution) | ||||||
![]() |
| ||||||
![]() | HYDROLASE/RNA / PAZ domain / platform domain / connector helix / siRNA / RNase III domain / endoribonuclease / pre-miRNA / HYDROLASE-RNA complex | ||||||
Function / homology | ![]() peripheral nervous system myelin formation / pre-miRNA binding / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / Small interfering RNA (siRNA) biogenesis / global gene silencing by mRNA cleavage / negative regulation of Schwann cell proliferation / ribonuclease III / positive regulation of myelination / apoptotic DNA fragmentation ...peripheral nervous system myelin formation / pre-miRNA binding / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / Small interfering RNA (siRNA) biogenesis / global gene silencing by mRNA cleavage / negative regulation of Schwann cell proliferation / ribonuclease III / positive regulation of myelination / apoptotic DNA fragmentation / miRNA metabolic process / nerve development / positive regulation of Schwann cell differentiation / RISC-loading complex / deoxyribonuclease I activity / RISC complex assembly / ribonuclease III activity / M-decay: degradation of maternal mRNAs by maternally stored factors / miRNA processing / siRNA binding / pre-miRNA processing / siRNA processing / RISC complex / MicroRNA (miRNA) biogenesis / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / RNA endonuclease activity / helicase activity / neuron projection morphogenesis / double-stranded RNA binding / protein domain specific binding / negative regulation of gene expression / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Tian, Y. / Simanshu, D.K. / Patel, D.J. | ||||||
![]() | ![]() Title: A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer. Authors: Tian, Y. / Simanshu, D.K. / Ma, J.B. / Park, J.E. / Heo, I. / Kim, V.N. / Patel, D.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 144.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 108.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 447.6 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ngbC ![]() 4ngcC ![]() 4ngdSC ![]() 4ngfC ![]() 4nggC ![]() 4nh3C ![]() 4nh6C ![]() 4nhaC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34928.336 Da / Num. of mol.: 1 Fragment: platform-PAZ-connector helix cassette (UNP residues 765-1065) Mutation: K822A/K823A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UPY3, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters |
---|---|
#2: RNA chain | Mass: 4401.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: siRNA |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.86 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M sodium formate, 0.1 M bicine, pH 8.1-8.5, 16-19% PEG5000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→30 Å / Num. all: 15564 / Num. obs: 15564 / % possible obs: 94.9 % / Redundancy: 3 % / Biso Wilson estimate: 66.25 Å2 / Rmerge(I) obs: 0.071 / Χ2: 2.362 / Net I/σ(I): 12.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4NGD Resolution: 2.55→27.964 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7303 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.85 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 236.92 Å2 / Biso mean: 83.3458 Å2 / Biso min: 41.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→27.964 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|