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Open data
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Basic information
Entry | Database: PDB / ID: 7voi | |||||||||
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Title | Structure of the human CNOT1(MIF4G)-CNOT6L-CNOT7 complex | |||||||||
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![]() | HYDROLASE / CCR4-NOT complex mRNA degradation / RNA BINDING PROTEIN | |||||||||
Function / homology | ![]() regulation of tyrosine phosphorylation of STAT protein / positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / RNA exonuclease activity / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway ...regulation of tyrosine phosphorylation of STAT protein / positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / RNA exonuclease activity / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / : / Deadenylation of mRNA / trophectodermal cell differentiation / deadenylation-dependent decapping of nuclear-transcribed mRNA / miRNA-mediated post-transcriptional gene silencing / regulatory ncRNA-mediated gene silencing / M-decay: degradation of maternal mRNAs by maternally stored factors / P-body assembly / nuclear retinoic acid receptor binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / peroxisomal membrane / positive regulation of 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 / intracellular non-membrane-bounded organelle / negative regulation of type I interferon-mediated signaling pathway / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of viral genome replication / nuclear estrogen receptor binding / P-body / mRNA processing / transcription corepressor activity / regulation of translation / 3'-5'-RNA exonuclease activity / DNA-binding transcription factor binding / defense response to virus / molecular adaptor activity / nuclear body / negative regulation of translation / nuclear speck / negative regulation of cell population proliferation / protein domain specific binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular space / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bartlam, M. / Zhang, Q. | |||||||||
Funding support | 2items
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![]() | ![]() Title: Structure of the human Ccr4-Not nuclease module using X-ray crystallography and electron paramagnetic resonance spectroscopy distance measurements. Authors: Zhang, Q. / Pavanello, L. / Potapov, A. / Bartlam, M. / Winkler, G.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 353.8 KB | Display | ![]() |
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PDB format | ![]() | 242.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451 KB | Display | ![]() |
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Full document | ![]() | 461.5 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4b8cS ![]() 4gmjS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32776.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 26628.979 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 63076.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0, 8% PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 4.38→50 Å / Num. obs: 10302 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 161.92 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.05 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 4.38→4.48 Å / Num. unique obs: 493 / CC1/2: 0.93 / Rpim(I) all: 0.177 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4B8C, 4GMJ Resolution: 4.38→38.74 Å / SU ML: 0.5167 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.5109 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 198.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.38→38.74 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 | Refine-ID: X-RAY DIFFRACTION
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