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Open data
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Basic information
Entry | Database: PDB / ID: 5vm9 | ||||||||||||||||||
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Title | Human Argonaute3 bound to guide RNA | ||||||||||||||||||
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![]() | Hydrolase/RNA / protein / complex / RNA Binding protein-RNA complex / Hydrolase-RNA complex | ||||||||||||||||||
Function / homology | ![]() RISC complex assembly => GO:0070922 / Wnt signaling pathway, calcium modulating pathway / : / endoribonuclease activity, cleaving miRNA-paired mRNA / 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 / RNA secondary structure unwinding ...RISC complex assembly => GO:0070922 / Wnt signaling pathway, calcium modulating pathway / : / endoribonuclease activity, cleaving miRNA-paired mRNA / 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 / RNA secondary structure unwinding / regulation of megakaryocyte differentiation / RISC-loading complex / regulation of stem cell proliferation / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA processing / miRNA-mediated gene silencing by inhibition of translation / pre-miRNA processing / RISC complex / Regulation of RUNX1 Expression and Activity / MicroRNA (miRNA) biogenesis / miRNA binding / mRNA catabolic process / Regulation of MECP2 expression and activity / Transcriptional Regulation by VENTX / condensed nuclear chromosome / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RNA endonuclease activity / TP53 Regulates Metabolic Genes / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / P-body / MAPK6/MAPK4 signaling / positive regulation of non-canonical NF-kappaB signal transduction / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / double-stranded RNA binding / Ca2+ pathway / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / single-stranded RNA binding / negative regulation of gene expression / positive regulation of gene expression / RNA binding / nucleoplasm / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() Insect cell expression vector pTIE1 (others) | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Park, M.S. / Nakanishi, K. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Human Argonaute3 has slicer activity. Authors: Park, M.S. / Phan, H.D. / Busch, F. / Hinckley, S.H. / Brackbill, J.A. / Wysocki, V.H. / Nakanishi, K. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 681.2 KB | Display | ![]() |
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PDB format | ![]() | 561.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482.7 KB | Display | ![]() |
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Full document | ![]() | 526.6 KB | Display | |
Data in XML | ![]() | 58.8 KB | Display | |
Data in CIF | ![]() | 79.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4olaS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 97645.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q9H9G7 #2: RNA chain | | Mass: 4188.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Insect cell expression vector pTIE1 (others) #3: RNA chain | | Mass: 4847.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Insect cell expression vector pTIE1 (others) |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM succinate-phosphateglycine buffer pH 4.4, 23% PEG2,000 and 4% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 3.28→67.48 Å / Num. obs: 28649 / % possible obs: 100 % / Redundancy: 13.6 % / Rpim(I) all: 0.086 / Net I/σ(I): 1.72 |
Reflection shell | Highest resolution: 3.28 Å / Rpim(I) all: 0.408 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4OLA Resolution: 3.28→67.476 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.11 / Stereochemistry target values: TWIN_LSQ_F Details: Author states that protein co-purified with endogenous microRNAs (miRNAs) which were from insect cells. This protein usually uptake the endogenous miRNAs during the overexpression and do not ...Details: Author states that protein co-purified with endogenous microRNAs (miRNAs) which were from insect cells. This protein usually uptake the endogenous miRNAs during the overexpression and do not release the RNA from the protein. They do not know the precise sequence or length of the RNA and the RNA were tightly bound to protein with the middle of the nucleotides disordered.
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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: 3.28→67.476 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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