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- EMDB-65155: Cryo-EM structure of SULTR-like phosphate distribution transporte... -

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Basic information

Entry
Database: EMDB / ID: EMD-65155
TitleCryo-EM structure of SULTR-like phosphate distribution transporter with phosphate
Map data
Sample
  • Complex: SULTR-like phosphate distribution transporter
    • Protein or peptide: Os06g0143700 protein
  • Ligand: PHOSPHATE ION
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 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: He H / Liu Y / Zhang J / Dong F / Liu Z
History
DepositionJun 24, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65155.png

Downloads & links

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Map

FileDownload / File: emd_65155.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-0.7392899 - 1.0831575
Average (Standard dev.)-0.00027572789 (±0.021031199)
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_65155_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65155_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
  • Ligand: PHOSPHATE ION

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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: #1
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 subsp. japonica (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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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
Component:
ConcentrationFormulaName
150.0 mmol/LNaClsodium chloride
25.0 mmol/LNaH2PO4/Na2HPO4Phosphate buffer
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: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 295132
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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