+Open data
-Basic information
Entry | Database: PDB / ID: 5ajd | ||||||
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Title | Not1 C-terminal domain in complex with Not4 | ||||||
Components |
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Keywords | TRANSCRIPTION / CCR4-NOT / NOT1 / NOT4 | ||||||
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 / deadenylation-independent decapping of nuclear-transcribed mRNA / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / ATPase activator activity / proteasomal protein catabolic process ...response to pheromone triggering conjugation with cellular fusion / negative regulation of cytoplasmic mRNA processing body assembly / pseudohyphal growth / CCR4-NOT core complex / deadenylation-independent decapping of nuclear-transcribed mRNA / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / ATPase activator activity / proteasomal protein catabolic process / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / P-body / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / molecular adaptor activity / negative regulation of translation / regulation of cell cycle / protein ubiquitination / regulation of transcription by RNA polymerase II / RNA binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 Å | ||||||
Authors | Bhaskar, V. / Basquin, J. / Conti, E. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Architecture of the Ubiquitylation Module of the Yeast Ccr4-not Complex. Authors: Bhaskar, V. / Basquin, J. / Conti, E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ajd.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ajd.ent.gz | 930.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ajd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ajd_validation.pdf.gz | 533.4 KB | Display | wwPDB validaton report |
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Full document | 5ajd_full_validation.pdf.gz | 551.6 KB | Display | |
Data in XML | 5ajd_validation.xml.gz | 99.8 KB | Display | |
Data in CIF | 5ajd_validation.cif.gz | 134.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/5ajd ftp://data.pdbj.org/pub/pdb/validation_reports/aj/5ajd | HTTPS FTP |
-Related structure data
Related structure data | 5aieC 4by6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 64811.562 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 1542-2094 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: CEN.PK113-7D / Plasmid: PEC-HIS-SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: N1P976, UniProt: P25655*PLUS #2: Protein | Mass: 7434.225 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 418-477 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Plasmid: PEC-HIS-GST / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P34909 Sequence details | RSM RESIDUES ARE LEFT OVER AFTER THE TAG CLEAVAGE GPDSM RESIDUES ARE LEFT OVER AFTER THE TAG CLEAVAGE | |
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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: 2.72 Å3/Da / Density % sol: 54.8 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 10% (W/V) PEG 4000, 0.02 M OF 1, 6-HEXANEDIOL, 0.02 M OF 1-BUTANOL, 0.02 M OF 1, 2-PROPANEDIOL (RACEMIC), 0.02 M OF 2-PROPANOL, 0T.02 M OF 1,4- BUTANEDIOL, 0.02 M OF 1,3-PROPANEDIOL, 0.1 M ...Details: 10% (W/V) PEG 4000, 0.02 M OF 1, 6-HEXANEDIOL, 0.02 M OF 1-BUTANOL, 0.02 M OF 1, 2-PROPANEDIOL (RACEMIC), 0.02 M OF 2-PROPANOL, 0T.02 M OF 1,4- BUTANEDIOL, 0.02 M OF 1,3-PROPANEDIOL, 0.1 M MOPS/HEPES-NA 7.5 AND 20% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2014 |
Radiation | Monochromator: MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 3.62→75.66 Å / Num. obs: 52676 / % possible obs: 99.8 % / Observed criterion σ(I): 1.3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.26 |
Reflection shell | Resolution: 3.62→3.75 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.37 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BY6 Resolution: 3.62→75.655 Å / SU ML: 0.65 / σ(F): 1.29 / Phase error: 40.54 / 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: 3.62→75.655 Å
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Refine LS restraints |
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LS refinement shell |
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