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- EMDB-65146: Cryo-EM structure of SULTR-like phosphate distribution transporter -

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Basic information

Entry
Database: EMDB / ID: EMD-65146
TitleCryo-EM structure of SULTR-like phosphate distribution transporter
Map data
Sample
  • Complex: SULTR-like phosphate distribution transporter
    • Protein or peptide: Os06g0143700 protein
KeywordsPhosphate distribution transporter / SULTR-like / Homodimer / TRANSPORT PROTEIN
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
Os06g0143700 protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice) / Oryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsLiu Y / Zhang J / He H / Liu Z
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65146.png

Downloads & links

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Map

FileDownload / File: emd_65146.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 400 pix.
= 292. Å		0.73 Å/pix.
x 400 pix.
= 292. Å		0.73 Å/pix.
x 400 pix.
= 292. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.85653675 - 1.2153736
Average (Standard dev.)-0.00028020664 (±0.022968045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 292.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65146_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_65146_half_map_2.map
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Sample components

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Entire : SULTR-like phosphate distribution transporter

EntireName: SULTR-like phosphate distribution transporter
Components
  • Complex: SULTR-like phosphate distribution transporter
    • Protein or peptide: Os06g0143700 protein

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Supramolecule #1: SULTR-like phosphate distribution transporter

SupramoleculeName: SULTR-like phosphate distribution transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)

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Macromolecule #1: Os06g0143700 protein

MacromoleculeName: Os06g0143700 protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 72.05418 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVVNNKVDSL SYDVEAPPAQ APTTPAVVSA PPTPRGEAPA MTTTAAAELH KVSVPERRST AKALRQRLAE VFFPDDPLHQ FKNQSSARR LVLALQYFFP IFHWGSDYSL RLLRSDVVSG LTIASLAIPQ GISYAKLANL PPIIGLYSSF VPPLIYSLLG S SRDLAVGP ...String:
MVVNNKVDSL SYDVEAPPAQ APTTPAVVSA PPTPRGEAPA MTTTAAAELH KVSVPERRST AKALRQRLAE VFFPDDPLHQ FKNQSSARR LVLALQYFFP IFHWGSDYSL RLLRSDVVSG LTIASLAIPQ GISYAKLANL PPIIGLYSSF VPPLIYSLLG S SRDLAVGP VSIASLVMGS MLRQAVSPDQ EPILYLQLAF TSTFFAGVFQ ASLGFLRLGF IVDFLSKATL TGFMGGAAII VS LQQLKGL LGIIHFTSQM GFVQVMHSVF KHHDEWAWQT ILMGVAFLAV LLTTRHISAR NPKLFWVSAA APLTSVIIST IIS FVSKAH GISVIGDLPK GLNPPSANML TFSGSYVGLA LNTGIMTGIL SLTEGIAVGR TFASINNYQV DGNKEMMAIG VMNM AGSCA SCYVTTGSFS RSAVNYSAGC KTAVSNIVMA SAVLVTLLFL MPLFHYTPNV ILSAIIITAV IGLIDVRGAA RLWKV DKLD FLACMAAFLG VLLVSVQMGL AIAVGISLFK ILLQVTRPNM VVKGVVPGTA SYRSMAQYRE AMRVPSFLVV GVESAI YFA NSMYLGERIM RFLREEDERA AKCNQCPVRC IILDMSAVAA IDTSGLDALA ELKKVLEKRN IELVLANPVG SVTERLY NS VVGKTFGSDR VFFSVAEAVA AAPHKTQP

UniProtKB: Os06g0143700 protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mmol/LNaClsodium chloride
25.0 mmol/LNH2C(CH2OH)3Trizma base
0.0001 m/vC47H88O22Lauryl maltose neopentyl glycol
1e-06 m/vC31H50O4Cholesteryl hemisuccinate

Details: 150mM NaCl, 25mM Phosphate Buffer, 0.0001m/v LMNG, 0.000001m/v CHS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 216928
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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