Crystal structure of the SPX domain of Chaetomium thermophilum Vtc4 in complex with inositol hexakisphosphate (InsP6).

Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

Starting Model: experimental
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Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains.

Wild, R.Gerasimaite, R.Jung, J.Y.Truffault, V.Pavlovic, I.Schmidt, A.Saiardi, A.Jessen, H.J.Poirier, Y.Hothorn, M.Mayer, A.

(2016) Science 352: 986-990

  • DOI: https://doi.org/10.1126/science.aad9858
  • Primary Citation of Related Structures:  
    5IIG, 5IIQ, 5IIT, 5IJH, 5IJJ, 5IJP

  • PubMed Abstract: 

    Phosphorus is a macronutrient taken up by cells as inorganic phosphate (P(i)). How cells sense cellular P(i) levels is poorly characterized. Here, we report that SPX domains--which are found in eukaryotic phosphate transporters, signaling proteins, and inorganic polyphosphate polymerases--provide a basic binding surface for inositol polyphosphate signaling molecules (InsPs), the concentrations of which change in response to P(i) availability. Substitutions of critical binding surface residues impair InsP binding in vitro, inorganic polyphosphate synthesis in yeast, and P(i) transport in Arabidopsis In plants, InsPs trigger the association of SPX proteins with transcription factors to regulate P(i) starvation responses. We propose that InsPs communicate cytosolic P(i) levels to SPX domains and enable them to interact with a multitude of proteins to regulate P(i) uptake, transport, and storage in fungi, plants, and animals.

  • Organizational Affiliation

    Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein201Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0057210
Find proteins for G0SCH1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SCH1 
Go to UniProtKB:  G0SCH1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SCH1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IHP

Download Ideal Coordinates CCD File 
C6 H18 O24 P6
Query on ACT

Download Ideal Coordinates CCD File 
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.75 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.2α = 90
b = 74.2β = 90
c = 74.42γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Rresearch CouncilSwitzerland310856

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references
  • Version 2.0: 2020-10-07
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description