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

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Basic information

Entry
Database: PDB / ID: 6qtx
TitleCrystal structure of an Arabidopsis WD40 domain in complex with a flowering transcription factor homolog
Components
  • E3 ubiquitin-protein ligase COP1
  • Zinc finger protein CONSTANS-LIKE 3
KeywordsPLANT PROTEIN / Complex
Function / homology
Function and homology information


regulation of photomorphogenesis / skotomorphogenesis / anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / red light signaling pathway / photoperiodism, flowering / regulation of flower development / red, far-red light phototransduction / regulation of stomatal movement ...regulation of photomorphogenesis / skotomorphogenesis / anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / red light signaling pathway / photoperiodism, flowering / regulation of flower development / red, far-red light phototransduction / regulation of stomatal movement / photomorphogenesis / nuclear ubiquitin ligase complex / entrainment of circadian clock / response to UV-B / Cul4-RING E3 ubiquitin ligase complex / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / sequence-specific DNA binding / transcription cis-regulatory region binding / protein ubiquitination / nuclear body / DNA-binding transcription factor activity / DNA repair / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
CCT domain / Zinc finger protein CONSTANS-like / CCT motif / CCT domain profile. / : / 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 ...CCT domain / Zinc finger protein CONSTANS-like / CCT motif / CCT domain profile. / : / 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. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / YVTN repeat-like/Quinoprotein amine dehydrogenase / Ring finger / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger RING-type profile. / Zinc finger, RING-type / WD domain, G-beta repeat / 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. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase COP1 / Zinc finger protein CONSTANS-LIKE 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 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 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase COP1
B: Zinc finger protein CONSTANS-LIKE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5956
Polymers38,2192
Non-polymers3764
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-38 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.465, 55.127, 103.538
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 Zinc finger protein CONSTANS-LIKE 3


Mass: 998.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SK53
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 222 / 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: 1.95 Å3/Da / Density % sol: 36.95 %
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 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.

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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: Sep 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.95→2.02 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.95→48.66 Å / SU ML: 0.1857 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.3229
RfactorNum. reflection% reflection
Rfree0.1897 1032 5.03 %
Rwork0.1389 --
obs0.1414 20512 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.91 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 22 222 2732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972575
X-RAY DIFFRACTIONf_angle_d1.0213490
X-RAY DIFFRACTIONf_chiral_restr0.0609390
X-RAY DIFFRACTIONf_plane_restr0.0064441
X-RAY DIFFRACTIONf_dihedral_angle_d17.29311541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.050.2491180.15522462X-RAY DIFFRACTION88.33
2.05-2.180.21421440.13262742X-RAY DIFFRACTION98.94
2.18-2.350.20271320.12672809X-RAY DIFFRACTION100
2.35-2.590.17781530.12822813X-RAY DIFFRACTION100
2.59-2.960.19981620.13382812X-RAY DIFFRACTION100
2.96-3.730.17391590.12882859X-RAY DIFFRACTION100
3.73-48.670.17391640.15812983X-RAY DIFFRACTION99.97

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