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Yorodumi- PDB-3adl: Structure of TRBP2 and its molecule implications for miRNA processing -
+Open data
-Basic information
Entry | Database: PDB / ID: 3adl | ||||||
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Title | Structure of TRBP2 and its molecule implications for miRNA processing | ||||||
Components |
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Keywords | GENE REGULATION/RNA / TRBP2 / miRNA processing / GENE REGULATION-RNA complex | ||||||
Function / homology | Function and homology information regulation of siRNA processing / regulation of miRNA processing / regulation of viral transcription / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / regulation of regulatory ncRNA processing / negative regulation of defense response to virus by host / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / global gene silencing by mRNA cleavage / RISC-loading complex ...regulation of siRNA processing / regulation of miRNA processing / regulation of viral transcription / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / regulation of regulatory ncRNA processing / negative regulation of defense response to virus by host / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / global gene silencing by mRNA cleavage / RISC-loading complex / RISC complex assembly / miRNA processing / siRNA binding / pre-miRNA processing / pre-mRNA binding / siRNA processing / RISC complex / MicroRNA (miRNA) biogenesis / miRNA binding / positive regulation of viral genome replication / protein sequestering activity / negative regulation of protein kinase activity / PKR-mediated signaling / double-stranded RNA binding / regulation of translation / nuclear body / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yuan, Y.A. / Chen, H.Y. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Structure of arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing Authors: Yang, S.W. / Chen, H.Y. / Yang, J. / Machida, S. / Chua, N.H. / Yuan, Y.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3adl.cif.gz | 42.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3adl.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 3adl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3adl_validation.pdf.gz | 466.4 KB | Display | wwPDB validaton report |
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Full document | 3adl_full_validation.pdf.gz | 467.5 KB | Display | |
Data in XML | 3adl_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 3adl_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/3adl ftp://data.pdbj.org/pub/pdb/validation_reports/ad/3adl | HTTPS FTP |
-Related structure data
Related structure data | 3adgC 3adiC 3adjC 1di2S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9931.413 Da / Num. of mol.: 1 / Fragment: DRBM 2 domain, UNP residues 161-231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TARBP2, TRBP / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15633 | ||
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#2: RNA chain | Mass: 3206.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic RNA #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: 2.55 Å3/Da / Density % sol: 51.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: AS, MgSO4, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Monochromator: 1.1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 8276 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.4 % / Rsym value: 0.046 / Net I/σ(I): 54 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 10 % / Mean I/σ(I) obs: 10.1 / Rsym value: 0.293 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DI2 Resolution: 2.2→25.84 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.866 / SU B: 13.165 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.304 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.367 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→25.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.204→2.262 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 9.8972 Å / Origin y: -4.1129 Å / Origin z: 13.0194 Å
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