+Open data
-Basic information
Entry | Database: PDB / ID: 4cv5 | ||||||
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Title | yeast NOT1 CN9BD-CAF40 complex | ||||||
Components |
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Keywords | CELL CYCLE | ||||||
Function / homology | Function and homology information response to pheromone triggering conjugation with cellular fusion / negative regulation of cytoplasmic mRNA processing body assembly / pseudohyphal growth / CCR4-NOT core complex / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / mRNA catabolic process / ATPase activator activity / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II ...response to pheromone triggering conjugation with cellular fusion / negative regulation of cytoplasmic mRNA processing body assembly / pseudohyphal growth / CCR4-NOT core complex / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / mRNA catabolic process / ATPase activator activity / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / P-body / molecular adaptor activity / negative regulation of translation / regulation of cell cycle / regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.807 Å | ||||||
Authors | Basquin, J. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cv5.cif.gz | 326.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cv5.ent.gz | 264.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cv5_validation.pdf.gz | 490.9 KB | Display | wwPDB validaton report |
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Full document | 4cv5_full_validation.pdf.gz | 501.1 KB | Display | |
Data in XML | 4cv5_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 4cv5_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/4cv5 ftp://data.pdbj.org/pub/pdb/validation_reports/cv/4cv5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 23529.105 Da / Num. of mol.: 2 / Fragment: RESIDUES 1071-1282 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288P / Plasmid: PEC_HIS_SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: P25655 #2: Protein | Mass: 36070.375 Da / Num. of mol.: 2 / Fragment: RESIDUES 54-373 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288P / Plasmid: PEC_HIS_SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: P53829 #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 74 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 50 MM HEPES PH 7.0, 3 M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.25472 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.25472 Å / Relative weight: 1 |
Reflection | Resolution: 3.81→48.29 Å / Num. obs: 22861 / % possible obs: 99.8 % / Observed criterion σ(I): 2.7 / Redundancy: 25.5 % / Biso Wilson estimate: 147.65 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 18 |
Reflection shell | Resolution: 3.81→4.01 Å / Redundancy: 23.3 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.7 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 3.807→48.292 Å / SU ML: 0.56 / σ(F): 1.35 / Phase error: 37.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.807→48.292 Å
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Refine LS restraints |
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LS refinement shell |
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