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Yorodumi- PDB-4nh3: Structure of human Dicer Platform-PAZ-Connector Helix cassette in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nh3 | ||||||
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Title | Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 13-mer siRNA having 5'-pU and UU-3' ends (2.6 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 / 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 / RISC-loading complex / positive regulation of Schwann cell differentiation / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.616 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 | 4nh3.cif.gz | 141.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nh3.ent.gz | 107.2 KB | Display | PDB format |
PDBx/mmJSON format | 4nh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nh3_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 4nh3_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 4nh3_validation.xml.gz | 12 KB | Display | |
Data in CIF | 4nh3_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/4nh3 ftp://data.pdbj.org/pub/pdb/validation_reports/nh/4nh3 | HTTPS FTP |
-Related structure data
Related structure data | 4ngbC 4ngcC 4ngdSC 4ngfC 4nggC 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: 4095.445 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: 2.76 Å3/Da / Density % sol: 55.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M sodium chloride, 0.1 M sodium citrate, pH 6.5, 18% PEG4000, 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-E / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 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: 2.6→30 Å / Num. obs: 13339 / % possible obs: 99.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 57.97 Å2 / Rmerge(I) obs: 0.107 / Χ2: 2.027 / Net I/σ(I): 7.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4NGD Resolution: 2.616→27.023 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.7171 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.92 / 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: 209.35 Å2 / Biso mean: 78.4335 Å2 / Biso min: 36.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.616→27.023 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: 9
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Refinement TLS params. | Method: refined / Origin x: 35.5759 Å / Origin y: 55.3756 Å / Origin z: 6.7324 Å
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Refinement TLS group |
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