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- PDB-9vl5: Cryo-EM structure of SULTR-like phosphate distribution transporte... -

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Basic information

Entry
Database: PDB / ID: 9vl5
TitleCryo-EM structure of SULTR-like phosphate distribution transporter with phosphate
ComponentsOs06g0143700 protein
KeywordsTRANSPORT PROTEIN / Phosphate distribution transporter / SULTR-like / Homodimer
Function / homology
Function and homology information


secondary active sulfate transmembrane transporter activity / transmembrane transporter activity / transmembrane transport / plasma 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 / Os06g0143700 protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsLiu, Y. / Zhang, J. / He, H. / Liu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32422041 China
CitationJournal: Sci China Life Sci / Year: 2026
Title: Structural and dynamic insights into SPDT for phosphorus allocation in rice.
Authors: Haitao He / Yan Liu / Jie Zhang / Xiaofeng Zheng / Lihuan Jiang / Zhangmeng Du / Jiaqi Zuo / Shuo Cao / Xuemei Peng / Zhiwen Zheng / Kun Li / Cuicui Shen / Yanke Chen / Ping Yin / Chuang ...Authors: Haitao He / Yan Liu / Jie Zhang / Xiaofeng Zheng / Lihuan Jiang / Zhangmeng Du / Jiaqi Zuo / Shuo Cao / Xuemei Peng / Zhiwen Zheng / Kun Li / Cuicui Shen / Yanke Chen / Ping Yin / Chuang Wang / Lizhong Xiong / Faming Dong / Zhu Liu /
Abstract: Phosphorus is essential for plants, absorbed as inorganic phosphate (Pi) and distributed via specialized transporters. The SULTR-like phosphorus distribution transporter (SPDT) preferentially ...Phosphorus is essential for plants, absorbed as inorganic phosphate (Pi) and distributed via specialized transporters. The SULTR-like phosphorus distribution transporter (SPDT) preferentially allocates phosphorus to developing grains-an energetically costly process that can potentially be attenuated without affecting crop yield and germination, positioning SPDT as a prime target for sustainable agriculture. Here, we report cryo-EM structures of rice SPDT in Pi-bound and apo states, uncovering an elevator-type transport mechanism. The transmembrane region segregates into a mobile Pi-binding core domain and a stationary gate domain. Pi coordination involves specific residues within the core domain, followed by an electropositive vestibule that extends from the binding pocket to the cytoplasm. Integrative structural and smFRET analyses demonstrate a dynamic mechanism regulating the transporter's conformational equilibrium. In this mechanism, the transporter's intracellular STAS domain acts as a bidirectional conformation-switch: (i) membrane-proximal binding stabilizes the inward-facing state via interactions with the core/gate domains, while (ii) dissociation enables reset to the outward-facing state. This dynamic coupling elucidates the regulatory mechanism of the STAS domain, highlighting its universally conserved function across the SulP, SULTR, and SLC26 families. Our findings provide a mechanistic blueprint for engineering phosphorus allocation in crops to enhance nutrient-use efficiency.
History
DepositionJun 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.1Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Os06g0143700 protein
A: Os06g0143700 protein
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 Os06g0143700 protein / SULTR-like Phosphate Distribution Transporter


Mass: 72054.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: SPDT, OsSULTR3;4, Os06g0143700, OSNPB_060143700 / Production host: Homo sapiens (human) / References: UniProt: Q5VQ79
#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: SULTR-like phosphate distribution transporter / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Details: 150mM NaCl, 25mM Phosphate Buffer, 0.0001m/v LMNG, 0.000001m/v CHS
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mmol/Lsodium chlorideNaCl1
225 mmol/LPhosphate bufferNaH2PO4/Na2HPO41
30.0001 m/vLauryl maltose neopentyl glycolC47H88O221
40.000001 m/vCholesteryl hemisuccinateC31H50O41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 295132 / Symmetry type: POINT
RefinementHighest resolution: 2.65 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0057916
ELECTRON MICROSCOPYf_angle_d0.71710753
ELECTRON MICROSCOPYf_dihedral_angle_d4.3491106
ELECTRON MICROSCOPYf_chiral_restr0.0441329
ELECTRON MICROSCOPYf_plane_restr0.0061328

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