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- PDB-9u9f: Cryo-EM structure of Oryza sativa phosphate transporter SPDT -

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Basic information

Entry
Database: PDB / ID: 9u9f
TitleCryo-EM structure of Oryza sativa phosphate transporter SPDT
ComponentsSULTR-like phosphorus distribution transporter
KeywordsTRANSPORT PROTEIN / phosphate transport / SPDT / SLC26 / SULTR / cryo-EM
Function / homology
Function and homology information


secondary active sulfate transmembrane transporter activity / membrane
Similarity search - Function
Sulphate anion transporter, conserved site / SLC26A transporters signature. / SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / SULTR-like phosphorus distribution transporter
Similarity search - Component
Biological speciesOryza sativa subsp. indica (long-grained rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsFang, S. / Zhang, X. / Zhang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32025020 China
CitationJournal: Sci Adv / Year: 2025
Title: Molecular mechanism underlying phosphate distribution by SULTR family transporter SPDT in .
Authors: Sunzhenhe Fang / Yang Zhao / Xue Zhang / Fang Yu / Peng Zhang /
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 ...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.
History
DepositionMar 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Oct 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: SULTR-like phosphorus distribution transporter
B: SULTR-like phosphorus distribution transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,2984
Polymers144,1082
Non-polymers1902
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein SULTR-like phosphorus distribution transporter


Mass: 72054.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice)
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: A0A1Y0BRS7
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of SPDT in GDN / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Oryza sativa subsp. indica (long-grained rice)
Source (recombinant)Organism: Insect cell expression vector pTIE1 (others)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.14_3260: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 314767 / Symmetry type: POINT

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