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Yorodumi- PDB-6qtw: Crystal structure of an Arabidopsis WD40 domain in complex with a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qtw | ||||||||||||
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Title | Crystal structure of an Arabidopsis WD40 domain in complex with a blue light photoreceptor | ||||||||||||
Components |
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Keywords | PLANT PROTEIN / Complex | ||||||||||||
Function / homology | Function and homology information detection of light stimulus / photoprotection / singlet oxygen-mediated programmed cell death / negative regulation of lateral root development / positive regulation of shade avoidance / positive regulation of systemic acquired resistance / regulation of secondary cell wall biogenesis / regulation of unidimensional cell growth / plant organ development / response to red light ...detection of light stimulus / photoprotection / singlet oxygen-mediated programmed cell death / negative regulation of lateral root development / positive regulation of shade avoidance / positive regulation of systemic acquired resistance / regulation of secondary cell wall biogenesis / regulation of unidimensional cell growth / plant organ development / response to red light / auxin transport / flavin adenine dinucleotide metabolic process / response to absence of light / circadian regulation of calcium ion oscillation / anthocyanin-containing compound metabolic process / response to strigolactone / regulation of meristem growth / response to low fluence blue light stimulus by blue low-fluence system / shade avoidance / positive regulation of flavonoid biosynthetic process / regulation of leaf morphogenesis / blue light signaling pathway / skotomorphogenesis / photoperiodism, flowering / red, far-red light phototransduction / positive regulation of anion channel activity / response to far red light / response to magnetism / phototropism / response to high light intensity / photomorphogenesis / stomatal movement / positive regulation of defense response to bacterium / response to blue light / regulation of stomatal movement / deoxyribodipyrimidine photo-lyase activity / blue light photoreceptor activity / nuclear ubiquitin ligase complex / regulation of hydrogen peroxide metabolic process / response to water deprivation / entrainment of circadian clock / Cul4-RING E3 ubiquitin ligase complex / response to UV-B / regulation of reactive oxygen species metabolic process / response to temperature stimulus / entrainment of circadian clock by photoperiod / response to light stimulus / FAD binding / circadian regulation of gene expression / RING-type E3 ubiquitin transferase / regulation of circadian rhythm / PML body / defense response / circadian rhythm / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / kinase activity / regulation of gene expression / proteasome-mediated ubiquitin-dependent protein catabolic process / protein autophosphorylation / nuclear body / protein kinase activity / protein ubiquitination / DNA repair / protein homodimerization activity / DNA binding / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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 | 6qtw.cif.gz | 243.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qtw.ent.gz | 162.8 KB | Display | PDB format |
PDBx/mmJSON format | 6qtw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qtw_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 6qtw_full_validation.pdf.gz | 459.9 KB | Display | |
Data in XML | 6qtw_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 6qtw_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/6qtw ftp://data.pdbj.org/pub/pdb/validation_reports/qt/6qtw | HTTPS FTP |
-Related structure data
Related structure data | 6qtoC 6qtqC 6qtrC 6qtsC 6qttC 6qtuC 6qtvC 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: 37220.645 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: 1208.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q43125 | ||||
#3: Chemical | #4: Chemical | #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: 1.98 Å3/Da / Density % sol: 37.86 % |
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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 1.25 M sodium malonate pH 7.5. |
-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: May 13, 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: 1.39→43.98 Å / Num. obs: 56339 / % possible obs: 99.88 % / Redundancy: 12.7 % / Biso Wilson estimate: 10.9 Å2 / Rrim(I) all: 0.0561 / Net I/σ(I): 11.78 |
Reflection shell | Resolution: 1.39→1.44 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IGO Resolution: 1.39→43.98 Å / SU ML: 0.1436 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.0895
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→43.98 Å
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Refine LS restraints |
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LS refinement shell |
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