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Open data
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Basic information
Entry | Database: PDB / ID: 6mfn | |||||||||
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Title | Human Argonaute2-miR-27a bound to HSUR1 target RNA | |||||||||
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![]() | HYDROLASE/RNA / RNA-binding protein / microRNA / target directed microRNA decay / HYDROLASE-RNA complex | |||||||||
Function / homology | ![]() : / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / miRNA-mediated gene silencing by mRNA destabilization / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation ...: / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / miRNA-mediated gene silencing by mRNA destabilization / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / negative regulation of amyloid precursor protein biosynthetic process / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / positive regulation of trophoblast cell migration / RNA secondary structure unwinding / miRNA metabolic process / RISC-loading complex / mRNA cap binding / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / mRNA 3'-UTR AU-rich region binding / miRNA-mediated gene silencing by inhibition of translation / regulatory ncRNA-mediated gene silencing / M-decay: degradation of maternal mRNAs by maternally stored factors / miRNA processing / RNA 7-methylguanosine cap binding / siRNA binding / pre-miRNA processing / siRNA processing / Regulation of RUNX1 Expression and Activity / RISC complex / MicroRNA (miRNA) biogenesis / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / miRNA binding / RNA polymerase II complex binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Regulation of MECP2 expression and activity / Nuclear events stimulated by ALK signaling in cancer / core promoter sequence-specific DNA binding / negative regulation of translational initiation / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RNA endonuclease activity / translation initiation factor activity / post-embryonic development / positive regulation of translation / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / P-body / MAPK6/MAPK4 signaling / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / double-stranded RNA binding / Ca2+ pathway / Estrogen-dependent gene expression / single-stranded RNA binding / translation / dendrite / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sheu-Gruttadauria, J. / MacRae, I.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Target-Directed MicroRNA Degradation. Authors: Sheu-Gruttadauria, J. / Pawlica, P. / Klum, S.M. / Wang, S. / Yario, T.A. / Schirle Oakdale, N.T. / Steitz, J.A. / MacRae, I.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 | ![]() | 364 KB | Display | ![]() |
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PDB format | ![]() | 291.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.9 KB | Display | ![]() |
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Full document | ![]() | 483.7 KB | Display | |
Data in XML | ![]() | 30.4 KB | Display | |
Data in CIF | ![]() | 42.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mdzC ![]() 6mfrC ![]() 6nitC ![]() 4w5oS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 97358.188 Da / Num. of mol.: 1 / Mutation: D669A, S387D, S824A, S828D, S831D, S834A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters |
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#2: RNA chain | Mass: 6665.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: RNA chain | Mass: 7028.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Chemical | ChemComp-IPH / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG3350, 50 mM Tris, pH 8.0, 20 mM magnesium chloride, 75 mM phenol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2017 |
Radiation | Monochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03323 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→28.59 Å / Num. obs: 37628 / % possible obs: 99.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.039 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4159 / Rpim(I) all: 0.323 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4W5O Resolution: 2.5→28.59 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→28.59 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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