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- EMDB-65602: Cryo-EM structure of Oryza sativa phosphate transporter SPDT in a... -

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Basic information

Entry
Database: EMDB / ID: EMD-65602
TitleCryo-EM structure of Oryza sativa phosphate transporter SPDT in apo-state
Map data
Sample
  • Complex: structure of SPDT in apo-state
    • Protein or peptide: SULTR-like phosphorus distribution transporter
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 Indica Group (long-grained rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 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
DepositionJul 29, 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_65602.png

Downloads & links

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Map

FileDownload / File: emd_65602.map.gz / Format: CCP4 / Size: 103 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.)
0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.241
Minimum - Maximum-4.0723567 - 4.2339087
Average (Standard dev.)0.00017661117 (±0.08725742)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half a

Fileemd_65602_half_map_1.map
Annotationhalf a
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half b

Fileemd_65602_half_map_2.map
Annotationhalf b
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : structure of SPDT in apo-state

EntireName: structure of SPDT in apo-state
Components
  • Complex: structure of SPDT in apo-state
    • Protein or peptide: SULTR-like phosphorus distribution transporter

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Supramolecule #1: structure of SPDT in apo-state

SupramoleculeName: structure of SPDT in apo-state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza sativa Indica Group (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 Indica Group (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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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: 30 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: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 114179
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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