+Open data
-Basic information
Entry | Database: PDB / ID: 5onb | ||||||
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Title | Drosophila Bag-of-marbles CBM peptide bound to human CAF40 | ||||||
Components |
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Keywords | GENE REGULATION / DEADENYLATION / CCR4-NOT / TRANSLATIONAL REPRESSION / TRANSLATION | ||||||
Function / homology | Function and homology information male germline stem cell symmetric division / cystoblast division / spectrosome / fusome organization / negative regulation of peptidoglycan recognition protein signaling pathway / germarium-derived female germ-line cyst formation / fusome / germ-line stem cell division / positive regulation of protein deubiquitination / cell competition in a multicellular organism ...male germline stem cell symmetric division / cystoblast division / spectrosome / fusome organization / negative regulation of peptidoglycan recognition protein signaling pathway / germarium-derived female germ-line cyst formation / fusome / germ-line stem cell division / positive regulation of protein deubiquitination / cell competition in a multicellular organism / CCR4-NOT core complex / female germ-line stem cell asymmetric division / spermatogonial cell division / CCR4-NOT complex / germ-line stem cell population maintenance / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of stem cell differentiation / sex differentiation / gamete generation / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / positive regulation of protein K63-linked deubiquitination / regulatory ncRNA-mediated gene silencing / positive regulation of smoothened signaling pathway / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of epidermal growth factor receptor signaling pathway / oogenesis / epidermal growth factor receptor binding / mRNA regulatory element binding translation repressor activity / nuclear receptor coactivator activity / ubiquitin binding / mRNA 3'-UTR binding / P-body / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytokine-mediated signaling pathway / positive regulation of peptidyl-serine phosphorylation / spermatogenesis / negative regulation of translation / cell cycle / protein domain specific binding / protein homodimerization activity / protein-containing complex / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Raisch, T. / Sgromo, A. / Backhaus, C. / Izaurralde, E. / Weichenrieder, O. | ||||||
Citation | Journal: RNA / Year: 2018 Title: DrosophilaBag-of-marbles directly interacts with the CAF40 subunit of the CCR4-NOT complex to elicit repression of mRNA targets. Authors: Sgromo, A. / Raisch, T. / Backhaus, C. / Keskeny, C. / Alva, V. / Weichenrieder, O. / Izaurralde, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5onb.cif.gz | 477.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5onb.ent.gz | 402.6 KB | Display | PDB format |
PDBx/mmJSON format | 5onb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/5onb ftp://data.pdbj.org/pub/pdb/validation_reports/on/5onb | HTTPS FTP |
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-Related structure data
Related structure data | 5onaC 2fv2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 31072.189 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The first six residues (GPHMLE) remain from the protease cleavage site and the linker. Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT9, RCD1, RQCD1 / Plasmid: PETMCN (PNEA) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: Q92600 #2: Protein/peptide | Mass: 2874.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P22745 #3: Chemical | ChemComp-GOL / | |
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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: 2.33 Å3/Da / Density % sol: 47.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM HEPES (pH 7.0) 200 mM CaCl2 15% PEG 6,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0396 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2015 / Details: focussing mirrors |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0396 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 26082 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 90.68 Å2 / Rsym value: 0.095 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 3→3.08 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1852 / Rsym value: 1.008 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FV2 Resolution: 3→46.73 Å / Cor.coef. Fo:Fc: 0.9351 / Cor.coef. Fo:Fc free: 0.8941 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.471
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Displacement parameters | Biso mean: 100.72 Å2
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Refine analyze | Luzzati coordinate error obs: 0.448 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3→46.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.12 Å / Total num. of bins used: 13
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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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