+Open data
-Basic information
Entry | Database: PDB / ID: 7voi | |||||||||
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Title | Structure of the human CNOT1(MIF4G)-CNOT6L-CNOT7 complex | |||||||||
Components |
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Keywords | HYDROLASE / CCR4-NOT complex mRNA degradation / RNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information regulation of tyrosine phosphorylation of STAT protein / positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / CCR4-NOT core complex / poly(A)-specific ribonuclease activity / 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 / CCR4-NOT core complex / poly(A)-specific ribonuclease activity / 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 / trophectodermal cell differentiation / deadenylation-dependent decapping of nuclear-transcribed mRNA / miRNA-mediated post-transcriptional gene silencing / Deadenylation of mRNA / P-body assembly / nuclear retinoic acid receptor binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / peroxisomal membrane / 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 / negative regulation of type I interferon-mediated signaling pathway / intracellular non-membrane-bounded organelle / 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 / negative regulation of translation / nuclear body / nuclear speck / protein domain specific binding / negative regulation of cell population proliferation / 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 / extracellular space / RNA binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.38 Å | |||||||||
Authors | Bartlam, M. / Zhang, Q. | |||||||||
Funding support | 2items
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Citation | Journal: Protein Sci. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7voi.cif.gz | 353.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7voi.ent.gz | 242.5 KB | Display | PDB format |
PDBx/mmJSON format | 7voi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/7voi ftp://data.pdbj.org/pub/pdb/validation_reports/vo/7voi | HTTPS FTP |
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-Related structure data
Related structure data | 4b8cS 4gmjS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: CNOT7, CAF1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UIV1, poly(A)-specific ribonuclease |
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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.) Homo sapiens (human) / Gene: CNOT1, CDC39, KIAA1007, NOT1, AD-005 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5YKK6 |
#3: Protein | Mass: 63076.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT6L, CCR4B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96LI5, poly(A)-specific ribonuclease |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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