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

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Basic information

Entry
Database: PDB / ID: 6qtv
TitleCrystal structure of an Arabidopsis WD40 domain in complex with an atypical bHLH transcription factor
Components
  • E3 ubiquitin-protein ligase COP1
  • Transcription factor HFR1
KeywordsPLANT PROTEIN / Complex
Function / homology
Function and homology information


anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / blue light signaling pathway / skotomorphogenesis / photoperiodism, flowering / red, far-red light phototransduction / response to far red light / photomorphogenesis / regulation of stomatal movement ...anthocyanin-containing compound metabolic process / shade avoidance / positive regulation of flavonoid biosynthetic process / blue light signaling pathway / skotomorphogenesis / photoperiodism, flowering / red, far-red light phototransduction / response to far red light / photomorphogenesis / regulation of stomatal movement / response to light intensity / nuclear ubiquitin ligase complex / entrainment of circadian clock / Cul4-RING E3 ubiquitin ligase complex / abscisic acid-activated signaling pathway / response to UV-B / transcription coregulator activity / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein dimerization activity / protein ubiquitination / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA repair / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase COP1 / Zinc finger, C3HC4 type (RING finger) / Helix-loop-helix DNA-binding domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. ...E3 ubiquitin-protein ligase COP1 / Zinc finger, C3HC4 type (RING finger) / Helix-loop-helix DNA-binding domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / 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 / Transcription factor HFR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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: Transcription factor HFR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9627
Polymers38,4722
Non-polymers4905
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-1 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.896, 55.089, 103.069
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 Transcription factor HFR1 / Basic helix-loop-helix protein 26 / bHLH 26 / Protein LONG HYPOCOTYL IN FAR-RED 1 / Protein REDUCED ...Basic helix-loop-helix protein 26 / bHLH 26 / Protein LONG HYPOCOTYL IN FAR-RED 1 / Protein REDUCED PHYTOCHROME SIGNALING / Reduced sensitivity to far-red light / Transcription factor EN 68 / bHLH transcription factor bHLH026


Mass: 1267.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FE22
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 1.96 Å3/Da / Density % sol: 37.17 %
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: 1.31→48.58 Å / Num. obs: 67056 / % possible obs: 99.76 % / Redundancy: 12.4 % / Biso Wilson estimate: 12.46 Å2 / Rrim(I) all: 0.0345 / Net I/σ(I): 16.09
Reflection shellResolution: 1.31→1.36 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: 1.31→48.58 Å / SU ML: 0.1241 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.5521
RfactorNum. reflection% reflection
Rfree0.1761 3236 4.83 %
Rwork0.1332 --
obs0.1353 67051 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.45 Å2
Refinement stepCycle: LAST / Resolution: 1.31→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 33 263 2784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712730
X-RAY DIFFRACTIONf_angle_d1.02473741
X-RAY DIFFRACTIONf_chiral_restr0.0866428
X-RAY DIFFRACTIONf_plane_restr0.006478
X-RAY DIFFRACTIONf_dihedral_angle_d17.81911044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.330.27571400.21192572X-RAY DIFFRACTION94.63
1.33-1.350.25961420.19782715X-RAY DIFFRACTION99.97
1.35-1.380.24721340.19312775X-RAY DIFFRACTION99.97
1.38-1.40.25251170.18172751X-RAY DIFFRACTION100
1.4-1.420.25671400.17812745X-RAY DIFFRACTION99.97
1.42-1.450.26031430.16392768X-RAY DIFFRACTION99.97
1.45-1.480.21251430.15982752X-RAY DIFFRACTION99.97
1.48-1.510.19251460.14622716X-RAY DIFFRACTION100
1.51-1.550.19681460.13362742X-RAY DIFFRACTION100
1.55-1.590.18451370.11992770X-RAY DIFFRACTION100
1.59-1.630.17841330.11562779X-RAY DIFFRACTION100
1.63-1.680.1671260.1122776X-RAY DIFFRACTION100
1.68-1.730.18431330.11482744X-RAY DIFFRACTION100
1.73-1.80.17031260.11792813X-RAY DIFFRACTION100
1.8-1.870.17031400.11822766X-RAY DIFFRACTION100
1.87-1.950.14811350.11552791X-RAY DIFFRACTION100
1.95-2.050.14121460.11042784X-RAY DIFFRACTION100
2.05-2.180.14481540.11032768X-RAY DIFFRACTION100
2.18-2.350.15821450.12362799X-RAY DIFFRACTION100
2.35-2.590.18461410.12852816X-RAY DIFFRACTION100
2.59-2.960.16821490.13392821X-RAY DIFFRACTION100
2.96-3.730.15461520.12522873X-RAY DIFFRACTION100
3.73-48.620.18221680.14952979X-RAY DIFFRACTION99.97

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