+Open data
-Basic information
Entry | Database: PDB / ID: 6oon | |||||||||||||||
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Title | Human Argonaute4 bound to guide RNA | |||||||||||||||
Components |
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Keywords | HYDROLASE/RNA / RNA / miRNA / RNA BINDING PROTEIN / HYDROLASE-RNA complex | |||||||||||||||
Function / homology | Function and homology information RISC complex assembly => GO:0070922 / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / synaptonemal complex assembly / male meiotic nuclear division / RNA secondary structure unwinding / miRNA metabolic process ...RISC complex assembly => GO:0070922 / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / synaptonemal complex assembly / male meiotic nuclear division / RNA secondary structure unwinding / miRNA metabolic process / RISC-loading complex / miRNA-mediated gene silencing by inhibition of translation / miRNA processing / pre-miRNA processing / regulation of cell morphogenesis / RISC complex / Regulation of RUNX1 Expression and Activity / miRNA binding / MicroRNA (miRNA) biogenesis / mRNA catabolic process / Regulation of MECP2 expression and activity / Transcriptional Regulation by VENTX / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / TP53 Regulates Metabolic Genes / MAPK6/MAPK4 signaling / P-body / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / male gonad development / double-stranded RNA binding / Ca2+ pathway / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / single-stranded RNA binding / negative regulation of apoptotic process / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||||||||
Authors | Park, M.S. / Brackbill, J.A. / Nakanishi, K. | |||||||||||||||
Funding support | United States, Japan, 4items
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Citation | Journal: Mol.Cell / Year: 2019 Title: Multidomain Convergence of Argonaute during RISC Assembly Correlates with the Formation of Internal Water Clusters. Authors: Park, M.S. / Araya-Secchi, R. / Brackbill, J.A. / Phan, H.D. / Kehling, A.C. / Abd El-Wahab, E.W. / Dayeh, D.M. / Sotomayor, M. / Nakanishi, K. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oon.cif.gz | 357.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oon.ent.gz | 285.1 KB | Display | PDB format |
PDBx/mmJSON format | 6oon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/6oon ftp://data.pdbj.org/pub/pdb/validation_reports/oo/6oon | HTTPS FTP |
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-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 97373.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGO4, EIF2C4, KIAA1567 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q9HCK5 |
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#2: RNA chain | Mass: 3859.432 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: Insect cell expression vector pTIE1 (others) |
#3: Water | ChemComp-HOH / |
Sequence details | The protein was co-purified with endogenous RNA from insect cells. Therefore, the precise sequence ...The protein was co-purified with endogenous RNA from insect cells. Therefore, the precise sequence or length of the RNA is unknown. The 5' end and 3' end of the RNA are tightly bound to the protein but the middle nucleotides were disordered. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG5000, 0.1 M MES, pH=6, 1 M LiCl, 100 mM Trimethylamine Hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.082 Å / Num. obs: 91128 / % possible obs: 98.9 % / Redundancy: 4.1 % / Net I/σ(I): 1.91 |
Reflection shell | Resolution: 1.9→1.95 Å / Num. unique obs: 14243 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OLA Resolution: 1.9→49.082 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→49.082 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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