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- PDB-4ngd: Structure of human Dicer Platform-PAZ-Connector Helix cassette in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ngd | ||||||
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Title | Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 12-mer siRNA having 5'-p and UU-3' ends (1.95 Angstrom resolution) | ||||||
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![]() | 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206.8 KB | Display | ![]() |
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PDB format | ![]() | 164.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.4 KB | Display | ![]() |
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Full document | ![]() | 461.1 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ngbC ![]() 4ngcC ![]() 4ngfC ![]() 4nggC ![]() 4nh3C ![]() 4nh5C ![]() 4nh6C ![]() 4nhaSC 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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2 | ![]()
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Unit cell |
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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 | ||||
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#2: RNA chain | Mass: 3789.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: siRNA | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M lithium sulfate, 0.1 M HEPES, pH 7.0-7.5, 16% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.95→50 Å / Num. obs: 28748 / % possible obs: 93.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 34.07 Å2 / Rmerge(I) obs: 0.071 / Χ2: 1.336 / Net I/σ(I): 10.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4NHA Resolution: 1.958→34.144 Å / Occupancy max: 1 / Occupancy min: 0.04 / FOM work R set: 0.8443 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 157.78 Å2 / Biso mean: 41.7759 Å2 / Biso min: 18.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.958→34.144 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 35.0424 Å / Origin y: 55.2709 Å / Origin z: 6.5643 Å
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Refinement TLS group |
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