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- PDB-6qtu: Crystal structure of Arabidopsis WD40 domain in complex with a BB... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qtu | ||||||||||||
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Title | Crystal structure of Arabidopsis WD40 domain in complex with a BBX transcription factor | ||||||||||||
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![]() | PLANT PROTEIN / Complex | ||||||||||||
Function / homology | ![]() positive regulation of shade avoidance / anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / seedling development / skotomorphogenesis / photoperiodism, flowering / response to karrikin / red, far-red light phototransduction / vegetative to reproductive phase transition of meristem ...positive regulation of shade avoidance / anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / seedling development / skotomorphogenesis / photoperiodism, flowering / response to karrikin / red, far-red light phototransduction / vegetative to reproductive phase transition of meristem / photomorphogenesis / regulation of stomatal movement / nuclear ubiquitin ligase complex / entrainment of circadian clock / Cul4-RING E3 ubiquitin ligase complex / response to UV-B / response to light stimulus / transcription coregulator activity / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / protein ubiquitination / DNA-binding transcription factor activity / DNA repair / regulation of DNA-templated transcription / DNA binding / zinc ion binding / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Hothorn, M. / Lau, K. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.5 KB | Display | ![]() |
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PDB format | ![]() | 165.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.9 KB | Display | ![]() |
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Full document | ![]() | 462.7 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qtoC ![]() 6qtqC ![]() 6qtrC ![]() 6qtsC ![]() 6qttC ![]() 6qtvC ![]() 6qtwC ![]() 6qtxC ![]() 5igoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37204.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P43254, RING-type E3 ubiquitin transferase | ||||
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#2: Protein/peptide | Mass: 1159.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.24 % |
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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: ![]() ![]() ![]() |
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: 1.3→48.48 Å / Num. obs: 67449 / % possible obs: 98.68 % / Redundancy: 12.5 % / Biso Wilson estimate: 13.24 Å2 / Rrim(I) all: 0.03442 / Net I/σ(I): 16.86 |
Reflection shell | Resolution: 1.3→1.34 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5IGO Resolution: 1.3→48.48 Å / SU ML: 0.1361 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.7246
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→48.48 Å
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Refine LS restraints |
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LS refinement shell |
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