+Open data
-Basic information
Entry | Database: PDB / ID: 5wea | |||||||||
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Title | Human Argonaute2 Helix-7 Mutant | |||||||||
Components |
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Keywords | HYDROLASE/RNA / Argonaute / RNA binding / RNA silencing / microRNA / HYDROLASE / 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 / 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 / RISC-loading complex / miRNA metabolic process / mRNA cap binding / RISC complex assembly / mRNA 3'-UTR AU-rich region binding / miRNA-mediated gene silencing by inhibition of translation / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA processing / RNA 7-methylguanosine cap binding / siRNA binding / pre-miRNA processing / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / siRNA processing / Regulation of RUNX1 Expression and Activity / RISC complex / 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 / 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 | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å | |||||||||
Authors | Schirle, N.T. / Klum, S.M. / MacRae, I.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: EMBO J. / Year: 2018 Title: Helix-7 in Argonaute2 shapes the microRNA seed region for rapid target recognition. Authors: Klum, S.M. / Chandradoss, S.D. / Schirle, N.T. / Joo, C. / 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 | 5wea.cif.gz | 339.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wea.ent.gz | 274.1 KB | Display | PDB format |
PDBx/mmJSON format | 5wea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wea_validation.pdf.gz | 475.3 KB | Display | wwPDB validaton report |
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Full document | 5wea_full_validation.pdf.gz | 489.1 KB | Display | |
Data in XML | 5wea_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 5wea_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/5wea ftp://data.pdbj.org/pub/pdb/validation_reports/we/5wea | HTTPS FTP |
-Related structure data
Related structure data | 4olaS 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
#1: Protein | Mass: 97300.000 Da / Num. of mol.: 1 / Mutation: M364A, I365A, S387D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGO2, EIF2C2 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters |
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#2: RNA chain | Mass: 2565.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-IPH / |
#4: Water | ChemComp-HOH / |
Sequence details | Authors state that the protein is bound to a heterogenous mix of RNAs, so RNA was modeled as a poly- ...Authors state that the protein is bound to a heterogenous mix of RNAs, so RNA was modeled as a poly-A (other than the 3'-terminal U), as that fits in the density. The central part of the RNA is disordered, and because the protein is bound to many different RNA sequences, a defined RNA sequence can not be provided. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 12% PEG 3350, 0.1 M phenol, 12% isopropanol, 0.1 M tris, pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→66 Å / Num. obs: 14855 / % possible obs: 94.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9 |
Reflection shell | Resolution: 3.1→3.2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.4 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OLA Resolution: 3.12→65.555 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 178.81 Å2 / Biso mean: 76.5462 Å2 / Biso min: 12.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.12→65.555 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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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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