+Open data
-Basic information
Entry | Database: PDB / ID: 1b7f | ||||||
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Title | SXL-LETHAL PROTEIN/RNA COMPLEX | ||||||
Components |
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Keywords | RNA-BINDING PROTEIN/RNA / SPLICING REGULATION / RNP DOMAIN / RNA COMPLEX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / RNA-BINDING PROTEIN-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 / regulation of stem cell division / sex determination ...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 / regulation of stem cell division / sex determination / negative regulation of RNA export from nucleus / poly-pyrimidine tract 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 / 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 / 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 / MIRAS / Resolution: 2.6 Å | ||||||
Authors | Handa, N. / Nureki, O. / Kurimoto, K. / Kim, I. / Sakamoto, H. / Shimura, Y. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Nature / Year: 1999 Title: Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Authors: Handa, N. / Nureki, O. / Kurimoto, K. / Kim, I. / Sakamoto, H. / Shimura, Y. / Muto, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b7f.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b7f.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 1b7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b7f_validation.pdf.gz | 403.5 KB | Display | wwPDB validaton report |
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Full document | 1b7f_full_validation.pdf.gz | 425.7 KB | Display | |
Data in XML | 1b7f_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1b7f_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/1b7f ftp://data.pdbj.org/pub/pdb/validation_reports/b7/1b7f | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99718, 0.04071, 0.06309), Vector: |
-Components
#1: RNA chain | Mass: 3707.112 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: ORIGIN OF THE SEQUENCE: DROSOPHILA MELANOGASTER, NUCLEUS #2: Protein | Mass: 18971.578 Da / Num. of mol.: 2 / Fragment: 2 RNP-DOMAINS / Mutation: F166Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cellular location: NUCLEUS / Plasmid: PK7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19339 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 17053 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Rsym value: 0.089 / Net I/σ(I): 12.03 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.73 % / Mean I/σ(I) obs: 1.62 / Rsym value: 0.411 / % possible all: 87.4 |
Reflection | *PLUS Num. measured all: 98612 / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS % possible obs: 87.4 % / Rmerge(I) obs: 0.411 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.6→15 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 15 Å / σ(F): 1 / % reflection Rfree: 10 % / Rfactor obs: 0.201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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