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- PDB-6mdz: Human Argonaute2-miR-122 bound to a target RNA with two central m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mdz | |||||||||
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Title | Human Argonaute2-miR-122 bound to a target RNA with two central mismatches (bu2) | |||||||||
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![]() | hydrolase/rna / RNA-binding protein / microRNA / target directed microRNA decay / HYDROLASE / 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 | ![]() unidentified (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 | ![]() | 371 KB | Display | ![]() |
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PDB format | ![]() | 295.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 508.5 KB | Display | ![]() |
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Full document | ![]() | 527.7 KB | Display | |
Data in XML | ![]() | 57.1 KB | Display | |
Data in CIF | ![]() | 77.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mfnC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 97358.188 Da / Num. of mol.: 2 / Mutation: S387D, D669A, D824A, 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 #2: RNA chain | Mass: 6788.021 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: RNA chain | Mass: 7218.399 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others) #4: Chemical | ChemComp-IPH / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG3350, 50mM Tris pH8, 20mM MgCl2, 75mM Phenol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→39.5 Å / Num. obs: 31940 / % possible obs: 99.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.08 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 3.4→3.58 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3 / Num. unique obs: 4579 / Rpim(I) all: 0.268 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4W5O Resolution: 3.4→38.293 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→38.293 Å
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Refine LS restraints |
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LS refinement shell |
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