[English] 日本語
![](img/lk-miru.gif)
- PDB-6qtx: Crystal structure of an Arabidopsis WD40 domain in complex with a... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6qtx | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of an Arabidopsis WD40 domain in complex with a flowering transcription factor homolog | ||||||||||||
![]() |
| ||||||||||||
![]() | PLANT PROTEIN / Complex | ||||||||||||
Function / homology | ![]() regulation of photomorphogenesis / red light signaling pathway / anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / skotomorphogenesis / photoperiodism, flowering / regulation of flower development / red, far-red light phototransduction / photomorphogenesis ...regulation of photomorphogenesis / red light signaling pathway / anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / skotomorphogenesis / photoperiodism, flowering / regulation of flower development / red, far-red light phototransduction / photomorphogenesis / regulation of stomatal movement / nuclear ubiquitin ligase complex / entrainment of circadian clock / Cul4-RING E3 ubiquitin ligase complex / response to UV-B / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / sequence-specific DNA binding / nuclear body / transcription cis-regulatory region binding / protein ubiquitination / DNA-binding transcription factor activity / DNA repair / zinc ion binding / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Hothorn, M. / Lau, K. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 160.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 106.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 453.4 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qtoC ![]() 6qtqC ![]() 6qtrC ![]() 6qtsC ![]() 6qttC ![]() 6qtuC ![]() 6qtvC ![]() 6qtwC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37220.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P43254, RING-type E3 ubiquitin transferase | ||||
---|---|---|---|---|---|
#2: Protein/peptide | Mass: 998.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.95 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.66 Å / Num. obs: 20513 / % possible obs: 98.21 % / Redundancy: 11.3 % / Biso Wilson estimate: 13.1 Å2 / Rrim(I) all: 0.03454 / Net I/σ(I): 24.92 |
Reflection shell | Resolution: 1.95→2.02 Å |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.95→48.66 Å / SU ML: 0.1857 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.3229
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→48.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|