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- PDB-9vky: Cryo-EM structure of SULTR-like phosphate distribution transporter -

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Basic information

Entry
Database: PDB / ID: 9vky
TitleCryo-EM structure of SULTR-like phosphate distribution transporter
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
Os06g0143700 protein
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.67 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: He, H. / Liu, Y. / Zhang, J. / Dong, F. / Liu, Z.
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

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Os06g0143700 protein
B: Os06g0143700 protein


Theoretical massNumber of molelcules
Total (without water)144,1082
Polymers144,1082
Non-polymers00
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 Japonica Group (Japanese rice)
Gene: SPDT, OsSULTR3;4, Os06g0143700, OSNPB_060143700 / Production host: Homo sapiens (human) / References: UniProt: Q5VQ79
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: all / 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/LTrizma baseNH2C(CH2OH)31
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: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 216928 / Symmetry type: POINT
RefinementHighest resolution: 2.67 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047920
ELECTRON MICROSCOPYf_angle_d0.64310758
ELECTRON MICROSCOPYf_dihedral_angle_d4.0421108
ELECTRON MICROSCOPYf_chiral_restr0.0421330
ELECTRON MICROSCOPYf_plane_restr0.0051330

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