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Yorodumi- PDB-5lsw: A CAF40-binding motif facilitates recruitment of the CCR4-NOT com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lsw | ||||||
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Title | A CAF40-binding motif facilitates recruitment of the CCR4-NOT complex to mRNAs targeted by Drosophila Roquin | ||||||
Components |
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Keywords | GENE REGULATION / DEADENYLATION / CCR4-NOT / TRANSLATIONAL REPRESSION / translation | ||||||
Function / homology | Function and homology information CCR4-NOT core complex / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / sex differentiation / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / 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 ...CCR4-NOT core complex / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / sex differentiation / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / 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 epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / regulation of mRNA stability / nuclear receptor coactivator activity / P-body / RING-type E3 ubiquitin transferase / cytokine-mediated signaling pathway / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytoplasmic stress granule / protein polyubiquitination / RNA stem-loop binding / ubiquitin protein ligase activity / double-stranded RNA binding / positive regulation of peptidyl-serine phosphorylation / ubiquitin-dependent protein catabolic process / negative regulation of translation / protein domain specific binding / mRNA binding / protein homodimerization activity / protein-containing complex / RNA binding / zinc ion binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Sgromo, A. / Raisch, T. / Bawankar, P. / Bhandari, D. / Chen, Y. / Kuzuoglu-Ozturk, D. / Weichenrieder, O. / Izaurralde, E. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: A CAF40-binding motif facilitates recruitment of the CCR4-NOT complex to mRNAs targeted by Drosophila Roquin. Authors: Sgromo, A. / Raisch, T. / Bawankar, P. / Bhandari, D. / Chen, Y. / Kuzuoglu-Ozturk, D. / Weichenrieder, O. / Izaurralde, E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lsw.cif.gz | 251.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lsw.ent.gz | 203.8 KB | Display | PDB format |
PDBx/mmJSON format | 5lsw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lsw_validation.pdf.gz | 474.5 KB | Display | wwPDB validaton report |
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Full document | 5lsw_full_validation.pdf.gz | 482.3 KB | Display | |
Data in XML | 5lsw_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 5lsw_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/5lsw ftp://data.pdbj.org/pub/pdb/validation_reports/ls/5lsw | HTTPS FTP |
-Related structure data
Related structure data | 2fv2S 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
#1: Protein | Mass: 31072.189 Da / Num. of mol.: 2 / Fragment: UNP residues 19-285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RQCD1, CNOT9, RCD1 / Plasmid: PETMCN(PNEA) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: Q92600 #2: Protein/peptide | Mass: 2277.593 Da / Num. of mol.: 2 / Fragment: UNP residues 790-810 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VV48 #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 2.49 Å3/Da / Density % sol: 50.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M Sodium Acetate pH 5.0 17.5 % (w/v) PEG 4000 0.1 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2014 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→46.8 Å / Num. obs: 34975 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 38.7 Å2 / CC1/2: 0.999 / Rsym value: 0.048 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.15→2.2 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.519 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FV2, CHAIN A Resolution: 2.15→46.769 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→46.769 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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