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- PDB-5kwn: The WD domain ofArabidopsis thaliana E3 Ubiquitin Ligase COP1 in ... -

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Basic information

Entry
Database: PDB / ID: 5kwn
TitleThe WD domain ofArabidopsis thaliana E3 Ubiquitin Ligase COP1 in complex with peptide from HY5
Components
  • E3 ubiquitin-protein ligase COP1
  • peptide 16-mer
KeywordsLigase/Peptide / photomorphogenesis E3 ligase WD domain transcription factor / Ligase-Peptide complex
Function / homology
Function and homology information


positive regulation of anthocyanin metabolic process / red or far-red light signaling pathway / regulation of photomorphogenesis / regulation of abscisic acid-activated signaling pathway / response to red light / anthocyanin-containing compound metabolic process / shade avoidance / positive gravitropism / positive regulation of flavonoid biosynthetic process / skotomorphogenesis ...positive regulation of anthocyanin metabolic process / red or far-red light signaling pathway / regulation of photomorphogenesis / regulation of abscisic acid-activated signaling pathway / response to red light / anthocyanin-containing compound metabolic process / shade avoidance / positive gravitropism / positive regulation of flavonoid biosynthetic process / skotomorphogenesis / photoperiodism, flowering / gibberellic acid mediated signaling pathway / red, far-red light phototransduction / response to far red light / photomorphogenesis / regulation of stomatal movement / nuclear ubiquitin ligase complex / entrainment of circadian clock / response to abscisic acid / positive regulation of circadian rhythm / Cul4-RING E3 ubiquitin ligase complex / abscisic acid-activated signaling pathway / response to UV-B / response to cold / protein-DNA complex / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / double-stranded DNA binding / protein ubiquitination / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / DNA repair / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / metal ion 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 superfamily / Basic-leucine zipper domain / YVTN repeat-like/Quinoprotein amine dehydrogenase ...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 superfamily / Basic-leucine zipper domain / 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
Transcription factor HY5 / E3 ubiquitin-protein ligase COP1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Arabidopsis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsUljon, S. / Blacklow, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)K08CA166227 United States
CitationJournal: To Be Published
Title: The COP1 WD domain in complex with HY5 peptide
Authors: Uljon, S. / Blacklow, S.
History
DepositionJul 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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
U: peptide 16-mer


Theoretical massNumber of molelcules
Total (without water)40,2572
Polymers40,2572
Non-polymers00
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-6 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.990, 55.176, 131.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11U-401-

HOH

Detailsdimer of protein and peptide, according to gel filtration

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Components

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


Mass: 38165.688 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: Trichoplusia ni (cabbage looper)
References: UniProt: P43254, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide peptide 16-mer


Mass: 2091.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis (plant) / References: UniProt: O24646*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: Sodium Chloride 0.3M Hepes 7.2 0.1M PEG 3350 25%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.42→38.775 Å / Num. obs: 66069 / % possible obs: 99 % / Redundancy: 2.9 % / Net I/σ(I): 22.97
Reflection shellResolution: 1.42→1.471 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.1526 / Mean I/σ(I) obs: 6.09 / CC1/2: 0.992 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IGO

5igo


Resolution: 1.42→38.775 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.88
RfactorNum. reflection% reflection
Rfree0.1736 3292 4.98 %
Rwork0.1596 --
obs0.1603 66066 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.42→38.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 0 375 2847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092585
X-RAY DIFFRACTIONf_angle_d1.0693514
X-RAY DIFFRACTIONf_dihedral_angle_d16.948935
X-RAY DIFFRACTIONf_chiral_restr0.101399
X-RAY DIFFRACTIONf_plane_restr0.006447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.44030.22221370.18442599X-RAY DIFFRACTION100
1.4403-1.46180.20051380.17942615X-RAY DIFFRACTION99
1.4618-1.48460.18491500.16952552X-RAY DIFFRACTION100
1.4846-1.5090.17981260.17712617X-RAY DIFFRACTION100
1.509-1.5350.17911390.16662616X-RAY DIFFRACTION99
1.535-1.56290.18721440.16312569X-RAY DIFFRACTION99
1.5629-1.5930.18971180.162599X-RAY DIFFRACTION99
1.593-1.62550.19311300.16552628X-RAY DIFFRACTION100
1.6255-1.66080.17191460.16372574X-RAY DIFFRACTION99
1.6608-1.69950.17221340.16432599X-RAY DIFFRACTION100
1.6995-1.7420.18021260.16052628X-RAY DIFFRACTION99
1.742-1.78910.15831360.16082620X-RAY DIFFRACTION99
1.7891-1.84170.21181330.16512610X-RAY DIFFRACTION99
1.8417-1.90110.17081250.15132574X-RAY DIFFRACTION99
1.9011-1.96910.18321580.15592608X-RAY DIFFRACTION99
1.9691-2.04790.19031350.14762616X-RAY DIFFRACTION99
2.0479-2.14110.16571380.15092618X-RAY DIFFRACTION99
2.1411-2.2540.13681440.14892609X-RAY DIFFRACTION99
2.254-2.39520.1691570.1622587X-RAY DIFFRACTION97
2.3952-2.58010.17321520.15742615X-RAY DIFFRACTION99
2.5801-2.83970.21361240.16542675X-RAY DIFFRACTION99
2.8397-3.25040.15621410.16322669X-RAY DIFFRACTION98
3.2504-4.09440.16581300.14932638X-RAY DIFFRACTION97
4.0944-38.78950.16071310.16482739X-RAY DIFFRACTION95

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