+Open data
-Basic information
Entry | Database: PDB / ID: 4ct7 | ||||||
---|---|---|---|---|---|---|---|
Title | CNOT9-CNOT1 complex with bound tryptophan | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / CNOT1-CN9DB-DOMAIN / TRYPTOPHANE / MES | ||||||
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 / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / sex 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 / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / sex differentiation / 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 epidermal growth factor receptor signaling pathway / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / epidermal growth factor receptor binding / nuclear receptor coactivator activity / nuclear estrogen receptor binding / P-body / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytokine-mediated signaling pathway / positive regulation of peptidyl-serine phosphorylation / negative regulation of translation / molecular adaptor activity / protein domain specific binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / extracellular space / RNA binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å | ||||||
Authors | Basquin, J. / Ozgur, S. / Conti, E. | ||||||
Citation | Journal: Mol.Cell / Year: 2014 Title: Structural and Biochemical Insights to the Role of the Ccr4-not Complex and Ddx6 ATPase in Microrna Repression. Authors: Mathys, H. / Basquin, J. / Ozgur, S. / Czarnocki-Cieciura, M. / Bonneau, F. / Aartse, A. / Dziembowski, A. / Nowotny, M. / Conti, E. / Filipowicz, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ct7.cif.gz | 223.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ct7.ent.gz | 177.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ct7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/4ct7 ftp://data.pdbj.org/pub/pdb/validation_reports/ct/4ct7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ct4C 4ct5C 4ct6C 4cv5C 2fv2S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 27470.666 Da / Num. of mol.: 1 / Fragment: CNOT1-CN9BD DOMAIN RESIDUES 1352-1594 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEC_HIS_GST / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A5YKK6 |
---|---|
#2: Protein | Mass: 30748.760 Da / Num. of mol.: 1 / Fragment: CNOT9, RESIDUES 16-285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEC_HIS_SUMO / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q92600 |
#3: Chemical | ChemComp-TRP / |
#4: Chemical | ChemComp-MES / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE |
---|---|
Crystal grow | pH: 6 Details: 20 % PEG 3350, 200 MM AMMONIUM SULFATE, 50 MM MES PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 18, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 1.897→48.27 Å / Num. obs: 54804 / % possible obs: 99.4 % / Observed criterion σ(I): 2.3 / Redundancy: 4.6 % / Biso Wilson estimate: 37.07 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.897→2.11 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / % possible all: 96.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FV2 Resolution: 1.897→48.271 Å / SU ML: 0.32 / σ(F): 1.21 / Phase error: 26.99 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.897→48.271 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|