- PDB-6qtw: Crystal structure of an Arabidopsis WD40 domain in complex with a... -
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Basic information
Entry
Database: PDB / ID: 6qtw
Title
Crystal structure of an Arabidopsis WD40 domain in complex with a blue light photoreceptor
Components
Cryptochrome-1
E3 ubiquitin-protein ligase COP1
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 / response to red light / auxin transport ...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 / response to red light / auxin transport / flavin adenine dinucleotide metabolic process / plant organ development / 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 high light intensity / response to far red light / response to magnetism / phototropism / 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 / regulation of hydrogen peroxide metabolic process / nuclear ubiquitin ligase complex / 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 / protein autophosphorylation / nuclear body / protein ubiquitination / protein kinase activity / DNA repair / protein homodimerization activity / DNA binding / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function
Cryptochrome C-terminal / Blue/Ultraviolet sensing protein C terminal / Cryptochrome, plant / E3 ubiquitin-protein ligase COP1 / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase ...Cryptochrome C-terminal / Blue/Ultraviolet sensing protein C terminal / Cryptochrome, plant / E3 ubiquitin-protein ligase COP1 / DNA photolyases class 1 signature 2. / Cryptochrome/DNA photolyase class 1, conserved site, C-terminal / DNA photolyases class 1 signature 1. / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / Zinc finger, C3HC4 type (RING finger) / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Ring finger / Rossmann-like alpha/beta/alpha sandwich fold / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta Similarity search - Domain/homology
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
#2: Protein/peptide
Cryptochrome-1 / / Atcry1 / Blue light photoreceptor / Protein BLUE LIGHT UNINHIBITED 1 / Protein ELONGATED HYPOCOTYL ...Atcry1 / Blue light photoreceptor / Protein BLUE LIGHT UNINHIBITED 1 / Protein ELONGATED HYPOCOTYL 4 / Protein OUT OF PHASE 2 / OOP2
Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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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 %
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.
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
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