9W3I

Cryo-EM structure of Oryza sativa phosphate transporter SPDT in apo-state

Summary for 9W3I

• Entry DOI: 10.2210/pdb9w3i/pdb
• EMDB information: 65602
• Descriptor: SULTR-like phosphorus distribution transporter (1 entity in total)
• Functional Keywords: phosphate transport, spdt, slc26, sultr, cryo-em, transport protein
• Biological source: Oryza sativa Indica Group (long-grained rice)
• Total number of polymer chains: 2
• Total formula weight: 144108.36

Authors

Fang, S.,Zhang, X.,Zhang, P. (deposition date: 2025-07-29, release date: 2025-10-22)

Primary citation

Fang, S.,Zhao, Y.,Zhang, X.,Yu, F.,Zhang, P.
Molecular mechanism underlying phosphate distribution by SULTR family transporter SPDT in Oryza sativa.
Sci Adv, 11:eady3442-eady3442, 2025

PubMed Abstract: Phosphorus (P) limitation severely affects crop yields. To address the molecular basis of inorganic phosphate (Pi) specific transport within the sulfate transporter (SULTR) family, we determined the cryo-electron microscopy structures of SULTR-like phosphorus distribution transporter (OsSPDT), a key Pi transporter for grain allocation, in apo- and Pi-binding states. OsSPDT forms a domain-swapped homodimer with each protomer containing an N-terminal domain (NTD), a transmembrane domain (TMD) divided into core and gate subdomains, and a C-terminal sulfate transporter and antisigma factor (STAS) domain. The structure adopts a cytoplasm-facing conformation with Pi coordinated at the core-gate interface. Key residues, including SPDT-unique Ser, mediate Pi specificity within the binding pocket, distinguishing it evolutionarily from sulfate transporters within the SULTR family. Domain-swapping and mutational studies demonstrate functional interdependence of the NTD, TMD, and STAS domains. This work elucidates Pi selectivity in plant SULTR transporters and provides a molecular basis for developing low-phytate rice via OsSPDT gene editing.

PubMed: 41071878
DOI: 10.1126/sciadv.ady3442

Experimental method

ELECTRON MICROSCOPY (3.16 Å)