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Yorodumi- PDB-4w5o: The Crystal Structure of Human Argonaute2 Bound to a Guide and Ta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w5o | ||||||
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Title | The Crystal Structure of Human Argonaute2 Bound to a Guide and Target RNA Containing Seed Pairing from 2-9 | ||||||
Components |
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Keywords | HYDROLASE/RNA / RNAi / AGO2 / Guide / Target / RNase / HYDROLASE-RNA complex | ||||||
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 / miRNA-mediated gene silencing by mRNA destabilization / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA 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 / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Regulation of PTEN mRNA translation / negative regulation of amyloid precursor protein biosynthetic process / Small interfering RNA (siRNA) biogenesis / positive regulation of trophoblast cell migration / Transcriptional Regulation by MECP2 / 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 / RNA 7-methylguanosine cap binding / pre-miRNA processing / regulation of synapse maturation / siRNA binding / siRNA processing / mRNA 3'-UTR AU-rich region binding / Regulation of MITF-M-dependent genes involved in apoptosis / M-decay: degradation of maternal mRNAs by maternally stored factors / TGFBR3 expression / P-body assembly / regulatory ncRNA-mediated gene silencing / RISC complex / Regulation of RUNX1 Expression and Activity / miRNA binding / MicroRNA (miRNA) biogenesis / 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 / 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 / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å | ||||||
Authors | Schirle, N.T. / MacRae, I.J. | ||||||
Citation | Journal: Science / Year: 2014 Title: Gene regulation. Structural basis for microRNA targeting. Authors: Schirle, N.T. / Sheu-Gruttadauria, J. / MacRae, I.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4w5o.cif.gz | 380.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w5o.ent.gz | 304 KB | Display | PDB format |
PDBx/mmJSON format | 4w5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4w5o_validation.pdf.gz | 498 KB | Display | wwPDB validaton report |
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Full document | 4w5o_full_validation.pdf.gz | 509.1 KB | Display | |
Data in XML | 4w5o_validation.xml.gz | 34.4 KB | Display | |
Data in CIF | 4w5o_validation.cif.gz | 51.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/4w5o ftp://data.pdbj.org/pub/pdb/validation_reports/w5/4w5o | HTTPS FTP |
-Related structure data
Related structure data | 4w5nC 4w5qC 4w5rC 4w5tC 4olaS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 97378.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGO2, EIF2C2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters |
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-RNA chain , 2 types, 2 molecules BD
#2: RNA chain | Mass: 6547.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: RNA chain | Mass: 3538.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 5 types, 443 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-IPH / #7: Chemical | ChemComp-PO4 / | #8: 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: 2.12 Å3/Da / Density % sol: 41.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: PEG 3350, Tris, Isopropanol, Phenol, Magnesium |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→39 Å / Num. obs: 80397 / % possible obs: 97.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.2 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OLA Resolution: 1.802→34.467 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.95 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.802→34.467 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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