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- PDB-6qtu: Crystal structure of Arabidopsis WD40 domain in complex with a BB... -

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Basic information

Entry
Database: PDB / ID: 6qtu
TitleCrystal structure of Arabidopsis WD40 domain in complex with a BBX transcription factor
Components
  • B-box zinc finger protein 24
  • E3 ubiquitin-protein ligase COP1
KeywordsPLANT PROTEIN / Complex
Function / homology
Function and homology information


positive regulation of shade avoidance / anthocyanin-containing compound metabolic process / response to karrikin / shade avoidance / positive regulation of flavonoid biosynthetic process / seedling development / skotomorphogenesis / photoperiodism, flowering / red, far-red light phototransduction / vegetative to reproductive phase transition of meristem ...positive regulation of shade avoidance / anthocyanin-containing compound metabolic process / response to karrikin / shade avoidance / positive regulation of flavonoid biosynthetic process / seedling development / skotomorphogenesis / photoperiodism, flowering / 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 / nuclear body / protein ubiquitination / DNA-binding transcription factor activity / DNA repair / regulation of DNA-templated transcription / DNA binding / zinc ion binding / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase COP1 / Zinc finger, C3HC4 type (RING finger) / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / 7 Propeller ...E3 ubiquitin-protein ligase COP1 / Zinc finger, C3HC4 type (RING finger) / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / 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 / 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 / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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 / B-box zinc finger protein 24
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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

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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: B-box zinc finger protein 24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6605
Polymers38,3642
Non-polymers2963
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-4 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.679, 54.992, 102.664
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: 37204.645 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 B-box zinc finger protein 24 / Salt tolerance protein


Mass: 1159.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q96288
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.24 %
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: 1.3→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 shellResolution: 1.3→1.34 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: 1.3→48.48 Å / SU ML: 0.1361 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.7246
RfactorNum. reflection% reflection
Rfree0.1759 3245 4.81 %
Rwork0.1412 --
obs0.1429 67439 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.67 Å2
Refinement stepCycle: LAST / Resolution: 1.3→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 20 239 2758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762732
X-RAY DIFFRACTIONf_angle_d1.06933741
X-RAY DIFFRACTIONf_chiral_restr0.0912427
X-RAY DIFFRACTIONf_plane_restr0.0068477
X-RAY DIFFRACTIONf_dihedral_angle_d17.33091039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.32561340.26222558X-RAY DIFFRACTION91.1
1.32-1.340.24751330.23982621X-RAY DIFFRACTION94.32
1.34-1.360.30241380.21692642X-RAY DIFFRACTION94.95
1.36-1.390.25271150.20752718X-RAY DIFFRACTION96.03
1.39-1.410.24161280.19912714X-RAY DIFFRACTION97.5
1.41-1.440.25551390.18912748X-RAY DIFFRACTION97.57
1.44-1.470.24611540.1762761X-RAY DIFFRACTION99.35
1.47-1.50.22731300.17222757X-RAY DIFFRACTION99.18
1.5-1.540.17631540.15522810X-RAY DIFFRACTION99.76
1.54-1.570.21991410.14122791X-RAY DIFFRACTION99.8
1.57-1.620.19431380.12822800X-RAY DIFFRACTION100
1.62-1.660.18881250.12752835X-RAY DIFFRACTION100
1.66-1.720.16591430.12342810X-RAY DIFFRACTION100
1.72-1.780.17221270.12242806X-RAY DIFFRACTION100
1.78-1.850.17081360.11932826X-RAY DIFFRACTION100
1.85-1.930.14071440.122837X-RAY DIFFRACTION100
1.93-2.040.14141450.11352844X-RAY DIFFRACTION100
2.04-2.160.1541520.11212799X-RAY DIFFRACTION100
2.16-2.330.15671510.1232853X-RAY DIFFRACTION100
2.33-2.570.16161440.13132858X-RAY DIFFRACTION99.97
2.57-2.940.16231500.13892877X-RAY DIFFRACTION99.97
2.94-3.70.16811500.13332900X-RAY DIFFRACTION100
3.7-48.510.17191740.15523029X-RAY DIFFRACTION99.88

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