+Open data
-Basic information
Entry | Database: PDB / ID: 5vm9 | ||||||||||||||||||
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Title | Human Argonaute3 bound to guide RNA | ||||||||||||||||||
Components |
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Keywords | Hydrolase/RNA / protein / complex / RNA Binding protein-RNA complex / Hydrolase-RNA complex | ||||||||||||||||||
Function / homology | Function and homology information 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 / regulatory ncRNA-mediated post-transcriptional gene silencing / regulation of stem cell proliferation / miRNA processing / pre-miRNA processing / miRNA-mediated gene silencing by inhibition of translation / RISC complex / miRNA binding / Regulation of RUNX1 Expression and Activity / 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 / RNA endonuclease activity / condensed nuclear chromosome / P-body / TP53 Regulates Metabolic Genes / MAPK6/MAPK4 signaling / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oncogene Induced Senescence / cytoplasmic ribonucleoprotein granule / Pre-NOTCH Transcription and Translation / positive regulation of non-canonical NF-kappaB signal transduction / 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 / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) Insect cell expression vector pTIE1 (others) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å | ||||||||||||||||||
Authors | Park, M.S. / Nakanishi, K. | ||||||||||||||||||
Funding support | United States, Japan, 5items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vm9.cif.gz | 681.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vm9.ent.gz | 561.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/5vm9 ftp://data.pdbj.org/pub/pdb/validation_reports/vm/5vm9 | 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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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.) Homo sapiens (human) / Gene: AGO3, EIF2C3 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: 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: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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