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Yorodumi- PDB-4ngb: Structure of human Dicer Platform-PAZ-Connector Helix cassette in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ngb | ||||||
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Title | Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 12-mer siRNA having UU-3' ends (2.25 Angstrom resolution) | ||||||
Components |
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Keywords | HYDROLASE/RNA / PAZ domain / platform domain / connector helix / siRNA / RNase III domain / endoribonuclease / pre-miRNA / HYDROLASE-RNA complex | ||||||
Function / homology | Function and homology information peripheral nervous system myelin formation / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / global gene silencing by mRNA cleavage / tRNA decay / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / negative regulation of Schwann cell proliferation / ribonuclease III / positive regulation of myelination / deoxyribonuclease I activity ...peripheral nervous system myelin formation / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / global gene silencing by mRNA cleavage / tRNA decay / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / negative regulation of Schwann cell proliferation / ribonuclease III / positive regulation of myelination / deoxyribonuclease I activity / apoptotic DNA fragmentation / miRNA metabolic process / nerve development / RISC-loading complex / positive regulation of Schwann cell differentiation / RISC complex assembly / miRNA processing / pre-miRNA processing / ribonuclease III activity / siRNA processing / siRNA binding / M-decay: degradation of maternal mRNAs by maternally stored factors / RISC complex / MicroRNA (miRNA) biogenesis / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / RNA endonuclease activity / neuron projection morphogenesis / helicase activity / 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 / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Simanshu, D.K. / Tian, Y. / Patel, D.J. | ||||||
Citation | Journal: Mol.Cell / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ngb.cif.gz | 147.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ngb.ent.gz | 111.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ngb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/4ngb ftp://data.pdbj.org/pub/pdb/validation_reports/ng/4ngb | HTTPS FTP |
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-Related structure data
Related structure data | 4ngcC 4ngdSC 4ngfC 4nggC 4nh3C 4nh5C 4nh6C 4nhaC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: DICER, DICER1, HERNA, KIAA0928 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.8 M sodium/potassium tartrate, 0.1 M sodium citrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0809 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→50 Å / Num. obs: 20573 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 34.94 Å2 / Rmerge(I) obs: 0.099 / Χ2: 2.25 / Net I/σ(I): 12.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4NGD Resolution: 2.25→31.995 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8204 / SU ML: 0.25 / σ(F): 1.34 / Phase error: 24.88 / 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: 83.4 Å2 / Biso mean: 38.6897 Å2 / Biso min: 14.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→31.995 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: 8
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Refinement TLS params. | Method: refined / Origin x: 35.0907 Å / Origin y: 55.5212 Å / Origin z: 6.642 Å
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Refinement TLS group |
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