Crystal structure of the oligomerisation domain of the transcription factor PHOSPHATE STARVATION RESPONSE 1 from Arabidopsis (crystal form 2)

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

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Inositol pyrophosphates promote the interaction of SPX domains with the coiled-coil motif of PHR transcription factors to regulate plant phosphate homeostasis.

Ried, M.K.Wild, R.Zhu, J.Pipercevic, J.Sturm, K.Broger, L.Harmel, R.K.Abriata, L.A.Hothorn, L.A.Fiedler, D.Hiller, S.Hothorn, M.

(2021) Nat Commun 12: 384-384

  • DOI: https://doi.org/10.1038/s41467-020-20681-4
  • Primary Citation of Related Structures:  
    6TO5, 6TO9, 6TOC

  • PubMed Abstract: 

    Phosphorus is an essential nutrient taken up by organisms in the form of inorganic phosphate (Pi). Eukaryotes have evolved sophisticated Pi sensing and signaling cascades, enabling them to stably maintain cellular Pi concentrations. Pi homeostasis is regulated by inositol pyrophosphate signaling molecules (PP-InsPs), which are sensed by SPX domain-containing proteins. In plants, PP-InsP-bound SPX receptors inactivate Myb coiled-coil (MYB-CC) Pi starvation response transcription factors (PHRs) by an unknown mechanism. Here we report that a InsP 8 -SPX complex targets the plant-unique CC domain of PHRs. Crystal structures of the CC domain reveal an unusual four-stranded anti-parallel arrangement. Interface mutations in the CC domain yield monomeric PHR1, which is no longer able to bind DNA with high affinity. Mutation of conserved basic residues located at the surface of the CC domain disrupt interaction with the SPX receptor in vitro and in planta, resulting in constitutive Pi starvation responses. Together, our findings suggest that InsP 8 regulates plant Pi homeostasis by controlling the oligomeric state and hence the promoter binding capability of PHRs via their SPX receptors.

  • Organizational Affiliation

    Institut de Biologie Structurale (IBS), 38044, Grenoble, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B [auth AAAB]
80Arabidopsis thalianaMutation(s): 0 
Gene Names: PHR1At4g28610T5F17.60
Find proteins for Q94CL7 (Arabidopsis thaliana)
Explore Q94CL7 
Go to UniProtKB:  Q94CL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94CL7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.05α = 90
b = 70.05β = 90
c = 80.17γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2021-01-13 
  • Deposition Author(s): Hothorn, M.

Funding OrganizationLocationGrant Number
European Research Council (ERC)Switzerland818696/INSPIRE
Swiss National Science FoundationSwitzerlandCRSII5_170925

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description