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Yorodumi- PDB-4qqb: Structural basis for the assembly of the SXL-UNR translation regu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qqb | ||||||
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Title | Structural basis for the assembly of the SXL-UNR translation regulatory complex | ||||||
Components |
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Keywords | TRANLATION/RNA / RNA binding domains / RNA recognition motif / RRM / cold shock domain / CSD / RNA binding / translation regulation / dosage compensation / TRANSCRIPTION-RNA complex / TRANLATION-RNA complex | ||||||
Function / homology | Function and homology information sex determination, primary response to X:A ratio / germarium-derived cystoblast division / epithelium regeneration / female sex determination / somatic sex determination / female germ-line sex determination / oocyte differentiation / imaginal disc growth / dosage compensation complex assembly / protein-RNA adaptor activity ...sex determination, primary response to X:A ratio / germarium-derived cystoblast division / epithelium regeneration / female sex determination / somatic sex determination / female germ-line sex determination / oocyte differentiation / imaginal disc growth / dosage compensation complex assembly / protein-RNA adaptor activity / regulation of stem cell division / sex determination / negative regulation of RNA export from nucleus / poly-pyrimidine tract binding / RISC complex binding / sex-chromosome dosage compensation / sex differentiation / alternative mRNA splicing, via spliceosome / negative regulation of receptor signaling pathway via JAK-STAT / poly(A) binding / positive regulation of smoothened signaling pathway / pre-mRNA binding / reciprocal meiotic recombination / regulation of mRNA splicing, via spliceosome / poly(U) RNA binding / lncRNA binding / regulation of alternative mRNA splicing, via spliceosome / oogenesis / negative regulation of mRNA splicing, via spliceosome / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / mRNA 3'-UTR binding / mRNA 5'-UTR binding / cell differentiation / protein stabilization / negative regulation of translation / ribonucleoprotein complex / mRNA binding / protein-containing complex / RNA binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Hennig, J. / Popowicz, G.M. / Sattler, M. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Structural basis for the assembly of the Sxl-Unr translation regulatory complex. Authors: Hennig, J. / Militti, C. / Popowicz, G.M. / Wang, I. / Sonntag, M. / Geerlof, A. / Gabel, F. / Gebauer, F. / Sattler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qqb.cif.gz | 124.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qqb.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/4qqb ftp://data.pdbj.org/pub/pdb/validation_reports/qq/4qqb | HTTPS FTP |
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-Related structure data
Related structure data | 1b7fS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | monomeric complex of three different entities (heterotrimer) |
-Components
#1: RNA chain | Mass: 5712.380 Da / Num. of mol.: 2 / Fragment: site F 18-mer / Source method: obtained synthetically / Details: synthetic RNA (purchased from IBA) #2: Protein | Mass: 19797.510 Da / Num. of mol.: 2 / Fragment: RRM1-RRM2, UNP residues 122-294 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sxl, Sx1, CG43770 / Production host: Escherichia coli (E. coli) / References: UniProt: P19339 #3: Protein | Mass: 8205.391 Da / Num. of mol.: 2 / Fragment: CSD1, UNP residues 185-252 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Unr, CG7015, Dmel_CG7015 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VSK3 |
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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: 5.4 Å3/Da / Density % sol: 77.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M LiSO4, PEG3350 1-5 %, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 36389 / Num. obs: 36315 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.8→2.85 Å / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B7F Resolution: 2.8→19.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.59 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.53 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 99.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
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