+Open data
-Basic information
Entry | Database: PDB / ID: 9bez | ||||||
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Title | MID domain of human Argo2 bound to RNA | ||||||
Components | Protein argonaute-2 | ||||||
Keywords | RNA BINDING PROTEIN / MID domain / Argonaute2 | ||||||
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 / 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 / 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 / P-body assembly / regulatory ncRNA-mediated gene silencing / 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 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of translational initiation / 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) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Harp, J.M. / Egli, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Curr Protoc / Year: 2024 Title: Structure and Stability of Ago2 MID-Nucleotide Complexes: All-in-One (Drop) His 6 -SUMO Tag Removal, Nucleotide Binding, and Crystal Growth. Authors: Lei, L. / Harp, J.M. / Chaput, J.C. / Wassarman, K. / Schlegel, M.K. / Manoharan, M. / Egli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bez.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bez.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9bez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bez_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 9bez_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 9bez_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 9bez_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/9bez ftp://data.pdbj.org/pub/pdb/validation_reports/be/9bez | HTTPS FTP |
-Related structure data
Related structure data | 9bf0C 9bf2C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15124.774 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGO2, EIF2C2 / Production host: Escherichia coli (E. coli) References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters #2: Chemical | Mass: 468.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H15N2O14P3 / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.46 Å3/Da / Density % sol: 49.95 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: Drops were equal volumes of 15 mg/ml protein and 2.1M DL-Malic acid. The reservoir was 2.1M DL-Malic acid. Using MRC drop plates. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.342 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Jan 23, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.342 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20.5 Å / Num. obs: 41796 / % possible obs: 99.04 % / Redundancy: 4.5 % / Biso Wilson estimate: 36.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.029 / Rrim(I) all: 0.068 / Net I/σ(I): 7.48 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique obs: 1612 / CC1/2: 0.247 / CC star: 0.629 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20.5 Å / SU ML: 0.2927 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 35.7579 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20.5 Å
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Refine LS restraints |
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LS refinement shell |
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