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- PDB-6qtw: Crystal structure of an Arabidopsis WD40 domain in complex with a... -

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Basic information

Entry
Database: PDB / ID: 6qtw
TitleCrystal structure of an Arabidopsis WD40 domain in complex with a blue light photoreceptor
Components
  • Cryptochrome-1
  • E3 ubiquitin-protein ligase COP1
KeywordsPLANT 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 anion channel activity / positive regulation of shade avoidance / positive regulation of systemic acquired resistance / regulation of secondary cell wall biogenesis / plant organ development / regulation of unidimensional cell growth ...detection of light stimulus / photoprotection / singlet oxygen-mediated programmed cell death / negative regulation of lateral root development / positive regulation of anion channel activity / positive regulation of shade avoidance / positive regulation of systemic acquired resistance / regulation of secondary cell wall biogenesis / plant organ development / regulation of unidimensional cell growth / flavin adenine dinucleotide metabolic process / response to absence of light / anthocyanin-containing compound metabolic process / response to strigolactone / regulation of meristem growth / response to red light / shade avoidance / positive regulation of flavonoid biosynthetic process / regulation of leaf morphogenesis / auxin transport / circadian regulation of calcium ion oscillation / response to low fluence blue light stimulus by blue low-fluence system / skotomorphogenesis / photoperiodism, flowering / red, far-red light phototransduction / blue light signaling pathway / response to magnetism / response to high light intensity / phototropism / stomatal movement / response to far red light / positive regulation of defense response to bacterium / regulation of stomatal movement / response to blue light / photomorphogenesis / regulation of hydrogen peroxide metabolic process / nuclear ubiquitin ligase complex / blue light photoreceptor activity / entrainment of circadian clock / response to water deprivation / Cul4-RING E3 ubiquitin ligase complex / response to UV-B / regulation of reactive oxygen species metabolic process / response to temperature stimulus / response to light stimulus / FAD binding / defense response / regulation of circadian rhythm / RING-type E3 ubiquitin transferase / circadian rhythm / ubiquitin-protein transferase activity / kinase activity / ubiquitin protein ligase activity / regulation of gene expression / protein autophosphorylation / protein kinase activity / protein ubiquitination / nuclear body / DNA repair / protein homodimerization activity / zinc ion binding / ATP binding / metal ion binding / identical protein 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. / Zinc finger, C3HC4 type (RING finger) / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain ...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. / Zinc finger, C3HC4 type (RING finger) / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Rossmann-like alpha/beta/alpha sandwich fold / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
MALONATE ION / E3 ubiquitin-protein ligase COP1 / Cryptochrome-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsHothorn, M. / Lau, K.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_175774 Switzerland
European Communitys Seventh Framework Programme310539 Switzerland
European Molecular Biology OrganizationALTF 493-2015 Switzerland
CitationJournal: 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
DepositionFeb 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase COP1
B: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8176
Polymers38,4292
Non-polymers3884
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-2 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.620, 55.142, 103.155
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein E3 ubiquitin-protein ligase COP1 / Constitutive photomorphogenesis protein 1 / RING-type E3 ubiquitin transferase COP1


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: 1208.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q43125
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.39→1.44 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IGO

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
RfactorNum. reflection% reflection
Rfree0.1723 2762 4.9 %
Rwork0.1361 --
obs0.1379 56337 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.64 Å2
Refinement stepCycle: LAST / Resolution: 1.39→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 26 280 2755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782658
X-RAY DIFFRACTIONf_angle_d1.05633629
X-RAY DIFFRACTIONf_chiral_restr0.0888412
X-RAY DIFFRACTIONf_plane_restr0.0062462
X-RAY DIFFRACTIONf_dihedral_angle_d16.84721015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.28681390.22972582X-RAY DIFFRACTION98.09
1.42-1.440.2661250.21572635X-RAY DIFFRACTION100
1.44-1.470.29361360.19522660X-RAY DIFFRACTION99.64
1.47-1.50.2431440.18022632X-RAY DIFFRACTION99.93
1.5-1.530.20411440.16392645X-RAY DIFFRACTION100
1.53-1.570.21111360.15022640X-RAY DIFFRACTION99.96
1.57-1.610.1981210.14042660X-RAY DIFFRACTION100
1.61-1.650.20831470.13562634X-RAY DIFFRACTION100
1.65-1.70.18161210.13222674X-RAY DIFFRACTION100
1.7-1.750.17331330.12862662X-RAY DIFFRACTION100
1.75-1.820.15271320.11942672X-RAY DIFFRACTION99.96
1.82-1.890.15721640.11772681X-RAY DIFFRACTION100
1.89-1.970.15091380.11732648X-RAY DIFFRACTION100
1.97-2.080.14751210.11322696X-RAY DIFFRACTION100
2.08-2.210.15151530.10962683X-RAY DIFFRACTION100
2.21-2.380.14321260.11852708X-RAY DIFFRACTION100
2.38-2.620.17071510.12232692X-RAY DIFFRACTION100
2.62-30.13771320.13142730X-RAY DIFFRACTION100
3-3.780.15511400.12872759X-RAY DIFFRACTION100
3.78-440.17861590.15562882X-RAY DIFFRACTION100

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