+Open data
-Basic information
Entry | Database: PDB / ID: 5aie | ||||||
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Title | Not4 ring domain in complex with Ubc4 | ||||||
Components |
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Keywords | LIGASE / SIGNALING PROTEIN / NOT4 RING DOMAIN / UBC4 / E2-E3 LIGASE | ||||||
Function / homology | Function and homology information CCR4-NOT core complex / deadenylation-independent decapping of nuclear-transcribed mRNA / CCR4-NOT complex / Peroxisomal protein import / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ribosome-associated ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme ...CCR4-NOT core complex / deadenylation-independent decapping of nuclear-transcribed mRNA / CCR4-NOT complex / Peroxisomal protein import / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ribosome-associated ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / proteasome binding / protein monoubiquitination / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / rescue of stalled ribosome / proteasomal protein catabolic process / ubiquitin binding / positive regulation of transcription elongation by RNA polymerase II / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / RNA binding / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aie.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aie.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 5aie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/5aie ftp://data.pdbj.org/pub/pdb/validation_reports/ai/5aie | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6796.774 Da / Num. of mol.: 1 / Fragment: RING DOMAIN, RESIDUES 30-83 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Plasmid: PEC-HIS-SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P34909 | ||
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#2: Protein | Mass: 17353.561 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Plasmid: PEC-HIS-SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P15731, ubiquitin-protein ligase | ||
#3: Chemical | Sequence details | RSM RESIDUES ARE LEFT OVER AFTER THE TAG CLEAVAGE TGSTGSTETG RESIDUES ARE THE ARTIFICIAL LINKER ...RSM RESIDUES ARE LEFT OVER AFTER THE TAG CLEAVAGE TGSTGSTETG | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.86 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 10% (W/V) PEG 8000, 0.02 M OF L-NA-GLUTAMATE, 0.02 M OF ALANINE (RACEMIC), 0.02 M OF GLYCINE, 0.02 M OF LYSINE HCL (RACEMIC), 0.02 M OF SERINE (RACEMIC), 0.1 M BICINE PH 8.5 AND 20% (W/V) ...Details: 10% (W/V) PEG 8000, 0.02 M OF L-NA-GLUTAMATE, 0.02 M OF ALANINE (RACEMIC), 0.02 M OF GLYCINE, 0.02 M OF LYSINE HCL (RACEMIC), 0.02 M OF SERINE (RACEMIC), 0.1 M BICINE PH 8.5 AND 20% (W/V) ETHYLENE GLYCOL AS CRYSTALLIZATION BUFFER AT ROOM TEMPERATURE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99995 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 10, 2014 |
Radiation | Monochromator: MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99995 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→53.56 Å / Num. obs: 6541 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.35 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 10 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.1 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→53.556 Å / SU ML: 0.45 / σ(F): 1.47 / Phase error: 38.34 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→53.556 Å
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Refine LS restraints |
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LS refinement shell |
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