+Open data
-Basic information
Entry | Database: PDB / ID: 5ona | ||||||
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Title | Drosophila Bag-of-marbles CBM peptide bound to human CAF40-CNOT1 | ||||||
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 / positive regulation of cytoplasmic mRNA processing body assembly ...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 / positive regulation of cytoplasmic mRNA processing body assembly / cell competition in a multicellular organism / CCR4-NOT core complex / female germ-line stem cell asymmetric division / armadillo repeat domain binding / spermatogonial cell division / CCR4-NOT complex / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / germ-line stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / positive regulation of stem cell differentiation / sex differentiation / gamete generation / trophectodermal cell differentiation / miRNA-mediated post-transcriptional gene silencing / Deadenylation of mRNA / nuclear retinoic acid receptor binding / 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 / peroxisomal membrane / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / nuclear estrogen receptor 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 / molecular adaptor activity / cell cycle / protein domain specific binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / extracellular space / RNA binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 5ona.cif.gz | 433.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ona.ent.gz | 360.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ona.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/5ona ftp://data.pdbj.org/pub/pdb/validation_reports/on/5ona | HTTPS FTP |
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-Related structure data
Related structure data | 5onbC 4cruS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27617.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The first 6 residues (GPHMLE) remain from the protease cleavage site and the linker. Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT1, CDC39, KIAA1007, NOT1, AD-005 / Plasmid: PETMCN (PNYC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: A5YKK6 #2: Protein | Mass: 31072.189 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The first 6 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 #3: Protein/peptide | Mass: 2874.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P22745 #4: Chemical | ChemComp-SO4 / #5: Chemical | |
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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: 3.51 Å3/Da / Density % sol: 64.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 1.5 M ammonium sulfate 20 mM MES (pH 6.0) 80 mM MES (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2015 / Details: DYNAMICALLY BENDABLE MIRRORS |
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: 2.7→50 Å / Num. obs: 48613 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 72.4 Å2 / Rsym value: 0.114 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3529 / Rsym value: 2.224 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CRU Resolution: 2.7→49.408 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→49.408 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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