6QTQ

Crystal structure of an Arabidopsis WD40 domain in complex with photoreceptor

  • Classification: PLANT PROTEIN
  • Organism(s): Arabidopsis thaliana
  • Expression System: Spodoptera frugiperda
  • Mutation(s): Yes 

  • Deposited: 2019-02-25 Released: 2019-07-10 
  • Deposition Author(s): Hothorn, M., Lau, K.
  • Funding Organization(s): Swiss National Science Foundation, European Communitys Seventh Framework Programme, European Molecular Biology Organization

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Plant photoreceptors and their signaling components compete for COP1 binding via VP peptide motifs.

Lau, K., Podolec, R., Chappuis, R., Ulm, R., Hothorn, M.

(2019) EMBO J 38: e102140-e102140

  • DOI: 10.15252/embj.2019102140
  • Primary Citation of Related Structures:  
    6QTO, 6QTQ, 6QTR, 6QTS, 6QTT, 6QTU, 6QTV, 6QTW, 6QTX

  • PubMed Abstract: 

    • Plants sense different parts of the sun's light spectrum using distinct photoreceptors, which signal through the E3 ubiquitin ligase COP1. Here, we analyze why many COP1-interacting transcription factors and photoreceptors harbor sequence-divergent Val-Pro (VP) motifs that bind COP1 with different binding affinities ...

    Plants sense different parts of the sun's light spectrum using distinct photoreceptors, which signal through the E3 ubiquitin ligase COP1. Here, we analyze why many COP1-interacting transcription factors and photoreceptors harbor sequence-divergent Val-Pro (VP) motifs that bind COP1 with different binding affinities. Crystal structures of the VP motifs of the UV-B photoreceptor UVR8 and the transcription factor HY5 in complex with COP1, quantitative binding assays, and reverse genetic experiments together suggest that UVR8 and HY5 compete for COP1. Photoactivation of UVR8 leads to high-affinity cooperative binding of its VP motif and its photosensing core to COP1, preventing COP1 binding to its substrate HY5. UVR8-VP motif chimeras suggest that UV-B signaling specificity resides in the UVR8 photoreceptor core. Different COP1-VP peptide motif complexes highlight sequence fingerprints required for COP1 targeting. The blue-light photoreceptors CRY1 and CRY2 also compete with transcription factors for COP1 binding using similar VP motifs. Thus, our work reveals that different photoreceptors and their signaling components compete for COP1 via a conserved mechanism to control different light signaling cascades.

    Organizational Affiliation: 

    Department of Botany and Plant Biology, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase COP1A330Arabidopsis thalianaMutation(s): 0 
Gene Names: COP1, At2g32950, T21L14.11
EC: 2.3.2.27
UniProt
Find proteins for P43254 (Arabidopsis thaliana)
Explore P43254 
Go to UniProtKB:  P43254
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43254
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ultraviolet-B receptor UVR8B9Arabidopsis thalianaMutation(s): 1 
Gene Names: UVR8, At5g63860, MGI19.7
UniProt
Find proteins for Q9FN03 (Arabidopsis thaliana)
Explore Q9FN03 
Go to UniProtKB:  Q9FN03
Entity Groups  
UniProt GroupQ9FN03
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO		A L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.678α = 90
b = 54.993β = 90
c = 102.892γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-02-25 
  • Released Date: 2019-07-10 
    • Deposition Author(s): Hothorn, M., Lau, K.
Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_175774
European Communitys Seventh Framework ProgrammeSwitzerland310539
European Molecular Biology OrganizationSwitzerlandALTF 493-2015

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references