EMD-61430

Single-particle
3.05 Å
EMD-61430 Deposition: 04/09/2024
Map released: 22/01/2025
Last modified: 29/01/2025
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-61430

Cryo-EM structure of the EXS domain of Arabidopsis thaliana phosphatetransporter PHO1;H1

EMD-61430

Single-particle
3.05 Å
EMD-61430 Deposition: 04/09/2024
Map released: 22/01/2025
Last modified: 29/01/2025
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Arabidopsis thaliana
Sample: EXS domain of Arabidopsis PHO1;H1
Fitted models: 9jf8 (Avg. Q-score: 0.508)

Deposition Authors: Fang S, Zhang X , Zhang P
Structural mechanism underlying PHO1;H1-mediated phosphate transport in Arabidopsis.
PUBMED: 39838070
DOI: doi:10.1038/s41477-024-01895-6
ISSN: 2055-0278
Abstract:
Arabidopsis PHOSPHATE 1 (AtPHO1) and its closest homologue AtPHO1;H1 are phosphate transporters that load phosphate into the xylem vessel for root-to-shoot translocation. AtPHO1 and AtPHO1;H1 are prototypical members of the unique SPX-EXS family, whose structural and molecular mechanisms remain elusive. In this study, we determined the cryogenic electron microscopy structure of AtPHO1;H1 binding with inorganic phosphate (Pi) and inositol hexakisphosphate in a closed conformation. Further molecular dynamic simulation and AlphaFold prediction support an open conformation. AtPHO1;H1 forms a domain-swapped homodimer that involves both the transmembrane ERD1/XPR1/SYG1 (EXS) domain and the cytoplasmic SYG1/Pho81/XPR1 (SPX) domain. The EXS domain presented by the SPX-EXS family represents a novel protein fold, and an independent substrate transport pathway and substrate-binding site are present in each EXS domain. Two gating residues, Trp719 and Tyr610, are identified above the substrate-binding site to control opening and closing of the pathway. The SPX domain features positively charged patches and/or residues at the dimer interface to accommodate inositol hexakisphosphate molecules, whose binding mediates dimerization and enhances AtPHO1;H1 activity. In addition, a C-terminal tail is required for AtPHO1;H1 activity. On the basis of structural and functional analysis, a working model for Pi efflux mediated by AtPHO1;H1 and its homologues was postulated, suggesting a channel-like mechanism. This study not only reveals the molecular and regulatory mechanism underlying Pi transport mediated by the unique SPX-EXS family, but also provides potential for crop engineering to enhance phosphorus-use efficiency in sustainable agriculture.