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- EMDB-63962: Cryo-EM structure of Oryza sativa phosphate transporter SPDT -

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Basic information

Entry
Database: EMDB / ID: EMD-63962
TitleCryo-EM structure of Oryza sativa phosphate transporter SPDT
Map datamap
Sample
  • Complex: Structure of SPDT in GDN
    • Protein or peptide: SULTR-like phosphorus distribution transporter
  • Ligand: PHOSPHATE ION
Keywordsphosphate transport / SPDT / SLC26 / SULTR / cryo-EM / TRANSPORT PROTEIN
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
SULTR-like phosphorus distribution transporter
Similarity search - Component
Biological speciesOryza sativa subsp. indica (long-grained rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsFang S / Zhang X / Zhang P
Funding support China, 1 items
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, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63962.png

Downloads & links

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Map

FileDownload / File: emd_63962.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 280 pix.
= 260.96 Å		0.93 Å/pix.
x 280 pix.
= 260.96 Å		0.93 Å/pix.
x 280 pix.
= 260.96 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.86
Minimum - Maximum-3.9524183 - 6.448712
Average (Standard dev.)0.0025323457 (±0.15220515)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 260.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half a

Fileemd_63962_half_map_1.map
Annotationhalf a
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half b

Fileemd_63962_half_map_2.map
Annotationhalf b
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Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of SPDT in GDN

EntireName: Structure of SPDT in GDN
Components
  • Complex: Structure of SPDT in GDN
    • Protein or peptide: SULTR-like phosphorus distribution transporter
  • Ligand: PHOSPHATE ION

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Supramolecule #1: Structure of SPDT in GDN

SupramoleculeName: Structure of SPDT in GDN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryza sativa subsp. indica (long-grained rice)

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Macromolecule #1: SULTR-like phosphorus distribution transporter

MacromoleculeName: SULTR-like phosphorus distribution transporter / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa subsp. indica (long-grained rice)
Molecular weightTheoretical: 72.05418 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
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: SULTR-like phosphorus distribution transporter

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Macromolecule #2: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 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: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 314767
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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