+Open data
-Basic information
Entry | Database: PDB / ID: 5jnb | ||||||||||||||||||||||||||||||
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Title | structure of GLD-2/RNP-8 complex | ||||||||||||||||||||||||||||||
Components |
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Keywords | TRANSFERASE / Translational control / Nucleotidyltransferase Poly(A) / Polymerase / RNA binding / C. elegans Germline development | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information polynucleotide adenylyltransferase activator activity / positive regulation of polynucleotide adenylyltransferase activity / : / poly(G) binding / RNA-directed RNA polymerase complex / positive regulation of meiosis I / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / P granule / embryo development ending in birth or egg hatching ...polynucleotide adenylyltransferase activator activity / positive regulation of polynucleotide adenylyltransferase activity / : / poly(G) binding / RNA-directed RNA polymerase complex / positive regulation of meiosis I / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / P granule / embryo development ending in birth or egg hatching / RNA polymerase complex / : / nucleus organization / regulation of cell division / regulation of alternative mRNA splicing, via spliceosome / positive regulation of mitotic nuclear division / meiotic cell cycle / mRNA processing / single-stranded RNA binding / enzyme binding / protein-containing complex / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.486 Å | ||||||||||||||||||||||||||||||
Authors | Nakel, K. / Bonneau, F. / Basquin, C. / Eckmann, C.R. / Conti, E. | ||||||||||||||||||||||||||||||
Funding support | Germany, 9items
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Citation | Journal: Rna / Year: 2016 Title: Structural basis for the antagonistic roles of RNP-8 and GLD-3 in GLD-2 poly(A)-polymerase activity. Authors: Nakel, K. / Bonneau, F. / Basquin, C. / Habermann, B. / Eckmann, C.R. / Conti, E. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jnb.cif.gz | 283.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jnb.ent.gz | 222.6 KB | Display | PDB format |
PDBx/mmJSON format | 5jnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/5jnb ftp://data.pdbj.org/pub/pdb/validation_reports/jn/5jnb | HTTPS FTP |
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-Related structure data
Related structure data | 4zrlS 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
-Protein , 2 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 38746.105 Da / Num. of mol.: 4 / Fragment: UNP residues 546-923 / Mutation: D668A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: gld-2, ZC308.1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O17087, polynucleotide adenylyltransferase #2: Protein | Mass: 8439.128 Da / Num. of mol.: 4 / Fragment: UNP residues 177-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: rnp-8, CELE_R119.7, R119.7 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O61711 |
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-Non-polymers , 4 types, 145 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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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: 2.74 Å3/Da / Density % sol: 55.17 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 18 % (v/v) PEG MME 550, 50 mM Potassium Nitrate, 60 mM Magnesium Nitrate, 30 mM Hepes pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.486→46.26 Å / Num. obs: 135156 / % possible obs: 95.6 % / Redundancy: 2.48 % / CC1/2: 0.993 / Rsym value: 0.088 / Net I/σ(I): 8.8 |
Reflection shell | Rsym value: 0.573 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZRL Resolution: 2.486→46.254 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 24.87 / Stereochemistry target values: ML
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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: 2.486→46.254 Å
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Refine LS restraints |
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LS refinement shell |
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