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Yorodumi- PDB-6qtr: Crystal structure of a mutant Arabidopsis WD40 domain in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qtr | ||||||||||||
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Title | Crystal structure of a mutant Arabidopsis WD40 domain in complex with a transcription factor | ||||||||||||
Components |
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Keywords | PLANT PROTEIN / Complex | ||||||||||||
Function / homology | Function and homology information positive regulation of anthocyanin metabolic process / red or far-red light signaling pathway / regulation of photomorphogenesis / regulation of abscisic acid-activated signaling pathway / response to red light / anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / positive gravitropism / skotomorphogenesis ...positive regulation of anthocyanin metabolic process / red or far-red light signaling pathway / regulation of photomorphogenesis / regulation of abscisic acid-activated signaling pathway / response to red light / anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / positive gravitropism / skotomorphogenesis / photoperiodism, flowering / gibberellic acid mediated signaling pathway / red, far-red light phototransduction / response to far red light / photomorphogenesis / regulation of stomatal movement / nuclear ubiquitin ligase complex / entrainment of circadian clock / response to abscisic acid / positive regulation of circadian rhythm / Cul4-RING E3 ubiquitin ligase complex / abscisic acid-activated signaling pathway / response to UV-B / response to cold / protein-DNA complex / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / double-stranded DNA binding / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / protein ubiquitination / DNA-binding transcription factor activity / DNA repair / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | ||||||||||||
Authors | Hothorn, M. / Lau, K. | ||||||||||||
Funding support | Switzerland, 3items
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Citation | Journal: Embo J. / Year: 2019 Title: Plant photoreceptors and their signaling components compete for COP1 binding via VP peptide motifs. Authors: Lau, K. / Podolec, R. / Chappuis, R. / Ulm, R. / Hothorn, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qtr.cif.gz | 250 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qtr.ent.gz | 167.3 KB | Display | PDB format |
PDBx/mmJSON format | 6qtr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/6qtr ftp://data.pdbj.org/pub/pdb/validation_reports/qt/6qtr | HTTPS FTP |
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-Related structure data
Related structure data | 6qtoC 6qtqC 6qtsC 6qttC 6qtuC 6qtvC 6qtwC 6qtxC 5igoS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37312.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: COP1, At2g32950, T21L14.11 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P43254, RING-type E3 ubiquitin transferase | ||||
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#2: Protein/peptide | Mass: 1350.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: O24646 | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.37 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop Details: 5 mg/mL of COP1 supplemented with 3 to 10 fold molar excess in peptide was mixed with two-fold (v/v) more mother liquor (1:2 ratio; protein:buffer) containing 2 M (NH4)2SO4 and 0.1 M HEPES ...Details: 5 mg/mL of COP1 supplemented with 3 to 10 fold molar excess in peptide was mixed with two-fold (v/v) more mother liquor (1:2 ratio; protein:buffer) containing 2 M (NH4)2SO4 and 0.1 M HEPES pH 7.4 or 0.1M Tris pH 8.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.03 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→43.74 Å / Num. obs: 57218 / % possible obs: 97.36 % / Redundancy: 13 % / Biso Wilson estimate: 10.14 Å2 / Rrim(I) all: 0.02722 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.37→1.42 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IGO Resolution: 1.37→43.74 Å / SU ML: 0.1091 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.9572
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→43.74 Å
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Refine LS restraints |
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LS refinement shell |
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