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Yorodumi- PDB-3ngn: Crystal structure of the human CNOT6L nuclease domain in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ngn | ||||||
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Title | Crystal structure of the human CNOT6L nuclease domain in complex with AMP | ||||||
Components | CCR4-NOT transcription complex subunit 6-like | ||||||
Keywords | HYDROLASE / PROTEIN-AMP COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA processing ...positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA processing / regulation of translation / positive regulation of cell population proliferation / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wang, H. / Morita, M. / Yang, W. / Bartlam, M. / Yamamoto, T. / Rao, Z. | ||||||
Citation | Journal: Embo J. / Year: 2010 Title: Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity. Authors: Wang, H. / Morita, M. / Yang, X. / Suzuki, T. / Yang, W. / Wang, J. / Ito, K. / Wang, Q. / Zhao, C. / Bartlam, M. / Yamamoto, T. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ngn.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ngn.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ngn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/3ngn ftp://data.pdbj.org/pub/pdb/validation_reports/ng/3ngn | HTTPS FTP |
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-Related 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: 45140.500 Da / Num. of mol.: 1 / Fragment: Nuclease Domain (UNP RESIDUES 158-555) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT6L, CCR4B / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q96LI5, Hydrolases; Acting on ester bonds | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Hepes, pH 7.5, 1.1M ammonium tartrate, 0.2M NDSB-201, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 22960 / Num. obs: 22869 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 54.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1120 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.828 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.226 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.791 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.401→2.463 Å / Total num. of bins used: 20
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