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- PDB-6qtr: Crystal structure of a mutant Arabidopsis WD40 domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 6qtr
TitleCrystal structure of a mutant Arabidopsis WD40 domain in complex with a transcription factor
Components
  • E3 ubiquitin-protein ligase COP1
  • Transcription factor HY5
KeywordsPLANT PROTEIN / Complex
Function / homology
Function and homology information


positive regulation of anthocyanin metabolic process / regulation of photomorphogenesis / regulation of abscisic acid-activated signaling pathway / skotomorphogenesis / anthocyanin-containing compound metabolic process / response to red light / red or far-red light signaling pathway / shade avoidance / positive regulation of flavonoid biosynthetic process / photoperiodism, flowering ...positive regulation of anthocyanin metabolic process / regulation of photomorphogenesis / regulation of abscisic acid-activated signaling pathway / skotomorphogenesis / anthocyanin-containing compound metabolic process / response to red light / red or far-red light signaling pathway / shade avoidance / positive regulation of flavonoid biosynthetic process / photoperiodism, flowering / red, far-red light phototransduction / gibberellic acid mediated signaling pathway / positive gravitropism / response to far red light / regulation of stomatal movement / photomorphogenesis / nuclear ubiquitin ligase complex / entrainment of circadian clock / response to abscisic acid / positive regulation of circadian rhythm / abscisic acid-activated signaling pathway / response to UV-B / Cul4-RING E3 ubiquitin ligase complex / response to cold / protein-DNA complex / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / nuclear body / protein ubiquitination / DNA-binding transcription factor activity / DNA repair / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Transcriptional activator Hac1/HY5 / E3 ubiquitin-protein ligase COP1 / bZIP transcription factor / Zinc finger, C3HC4 type (RING finger) / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Zinc finger, RING-type, conserved site ...Transcriptional activator Hac1/HY5 / E3 ubiquitin-protein ligase COP1 / bZIP transcription factor / Zinc finger, C3HC4 type (RING finger) / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / 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
Transcription factor HY5 / E3 ubiquitin-protein ligase COP1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase COP1
B: Transcription factor HY5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9485
Polymers38,6632
Non-polymers2843
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-29 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.260, 55.059, 103.483
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: 37312.762 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 HY5 / Protein LONG HYPOCOTYL 5 / bZIP transcription factor 56 / AtbZIP56


Mass: 1350.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: O24646
#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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 1.9 Å3/Da / Density % sol: 35.37 %
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: Nov 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.37→43.74 Å / Num. obs: 57218 / % possible obs: 97.36 % / Redundancy: 13 % / Biso Wilson estimate: 10.14 Å2 / Rrim(I) all: 0.02722 / Net I/σ(I): 22.6
Reflection shellResolution: 1.37→1.42 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: 1.37→43.74 Å / SU ML: 0.1091 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.9572
RfactorNum. reflection% reflection
Rfree0.1613 2853 4.99 %
Rwork0.12 --
obs0.122 57217 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.69 Å2
Refinement stepCycle: LAST / Resolution: 1.37→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 0 16 275 2824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742712
X-RAY DIFFRACTIONf_angle_d1.05963698
X-RAY DIFFRACTIONf_chiral_restr0.0863417
X-RAY DIFFRACTIONf_plane_restr0.0065467
X-RAY DIFFRACTIONf_dihedral_angle_d19.25241010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.21461370.14832537X-RAY DIFFRACTION92.21
1.39-1.420.19681210.13872566X-RAY DIFFRACTION92.21
1.42-1.450.2091250.12692582X-RAY DIFFRACTION93.44
1.45-1.480.18791340.11872581X-RAY DIFFRACTION94.07
1.48-1.510.16891290.11332631X-RAY DIFFRACTION95.07
1.51-1.540.16961340.11212626X-RAY DIFFRACTION95.17
1.54-1.580.1461440.10892672X-RAY DIFFRACTION96.67
1.58-1.620.16441290.1052708X-RAY DIFFRACTION97.09
1.62-1.670.14591490.10782711X-RAY DIFFRACTION98.01
1.67-1.730.13831500.10452720X-RAY DIFFRACTION98.36
1.73-1.790.13561450.10652729X-RAY DIFFRACTION98.73
1.79-1.860.16241460.10492735X-RAY DIFFRACTION98.94
1.86-1.940.13711380.10652749X-RAY DIFFRACTION99.14
1.94-2.050.14651470.10192759X-RAY DIFFRACTION98.94
2.05-2.170.1311540.10312772X-RAY DIFFRACTION99.63
2.17-2.340.14641500.10922777X-RAY DIFFRACTION99.52
2.34-2.580.17721480.12042814X-RAY DIFFRACTION99.8
2.58-2.950.17921750.12672814X-RAY DIFFRACTION99.87
2.95-3.720.14961530.12652870X-RAY DIFFRACTION99.93
3.72-43.760.18461450.14763011X-RAY DIFFRACTION100

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