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Yorodumi- PDB-3qx8: Crystal structure of MID domain from hAGO2 in complex with m7GpppG -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qx8 | ||||||
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Title | Crystal structure of MID domain from hAGO2 in complex with m7GpppG | ||||||
Components | Protein argonaute-2 | ||||||
Keywords | RNA BINDING PROTEIN / Rossmann-like folde / RNA binding / small RNA | ||||||
Function / homology | Function and homology information : / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / Regulation of CDH11 mRNA translation by microRNAs / miRNA-mediated gene silencing by mRNA destabilization / 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 / Regulation of CDH11 mRNA translation by microRNAs / miRNA-mediated gene silencing by mRNA destabilization / 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 / RISC-loading complex / miRNA metabolic process / mRNA cap binding / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA processing / miRNA-mediated gene silencing by inhibition of translation / regulation of synapse maturation / pre-miRNA processing / RNA 7-methylguanosine cap binding / mRNA 3'-UTR AU-rich region binding / siRNA binding / siRNA processing / Regulation of MITF-M-dependent genes involved in apoptosis / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / P-body assembly / RISC complex / Regulation of RUNX1 Expression and Activity / MicroRNA (miRNA) biogenesis / miRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / Transcriptional regulation by small RNAs / TP53 Regulates Metabolic Genes / 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 / postsynapse / single-stranded RNA binding / translation / glutamatergic synapse / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Frank, F. / Fabian, M.R. / Stepinski, J. / Jemielity, J. / Darzynkiewicz, E. / Sonenberg, N. / Nagar, B. | ||||||
Citation | Journal: Embo Rep. / Year: 2011 Title: Structural analysis of 5'-mRNA-cap interactions with the human AGO2 MID domain. Authors: Frank, F. / Fabian, M.R. / Stepinski, J. / Jemielity, J. / Darzynkiewicz, E. / Sonenberg, N. / Nagar, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qx8.cif.gz | 93.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qx8.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 3qx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qx8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3qx8_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3qx8_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 3qx8_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/3qx8 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/3qx8 | HTTPS FTP |
-Related structure data
Related structure data | 3qx9C 3lucS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 15325.955 Da / Num. of mol.: 3 / Fragment: unp residues 439-575 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2C2, AGO2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKV8 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M imidazole, 0.2 M NaCl, 0.46 M NaH2PO4, 1.84 M K2HPO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 23, 2010 |
Radiation | Monochromator: Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 20712 / Num. obs: 17438 / % possible obs: 84.2 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3LUC Resolution: 2.3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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