+Open data
-Basic information
Entry | Database: PDB / ID: 8bfi | ||||||
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Title | human CNOT1-CNOT10-CNOT11 module | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / N-Terminal module CCR4-NOT complex | ||||||
Function / homology | Function and homology information positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / 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 ...positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / 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 / miRNA-mediated post-transcriptional gene silencing / Deadenylation of mRNA / nuclear retinoic acid receptor binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / 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 / mRNA catabolic process / nuclear estrogen receptor binding / P-body / regulation of translation / negative regulation of translation / molecular adaptor activity / protein domain specific binding / negative regulation of transcription by RNA polymerase II / extracellular space / RNA binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Basquin, J. / Ozgur, S. / Conti, E. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Cell Rep / Year: 2023 Title: The human CNOT1-CNOT10-CNOT11 complex forms a structural platform for protein-protein interactions. Authors: Mauxion, F. / Basquin, J. / Ozgur, S. / Rame, M. / Albrecht, J. / Schafer, I. / Seraphin, B. / Conti, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bfi.cif.gz | 368.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bfi.ent.gz | 249.5 KB | Display | PDB format |
PDBx/mmJSON format | 8bfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/8bfi ftp://data.pdbj.org/pub/pdb/validation_reports/bf/8bfi | HTTPS FTP |
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-Related structure data
Related structure data | 8bfhC 8bfjC C: citing same article (ref.) |
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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: 88423.750 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 (E. coli) / References: UniProt: A5YKK6 |
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#2: Protein | Mass: 79251.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H9A5 |
#3: Protein | Mass: 50624.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT11, C2orf29, C40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKZ1 |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.84 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 5% (w/v) PEG 3500, 2% (v/v) isopropanol, 0.1 M MES pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3→45.77 Å / Num. obs: 89839 / % possible obs: 99.96 % / Redundancy: 68.3 % / Biso Wilson estimate: 85.69 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.3212 / Net I/σ(I): 22.31 |
Reflection shell | Resolution: 3→3.107 Å / Num. unique obs: 4548 / CC1/2: 0.435 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→45.77 Å / SU ML: 0.4862 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 31.0387 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 106.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→45.77 Å
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Refine LS restraints |
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LS refinement shell |
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