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- PDB-9nnc: Cryo-EM structure of Serendipita indica sulfate transporter SiSul... -

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Basic information

Entry
Database: PDB / ID: 9nnc
TitleCryo-EM structure of Serendipita indica sulfate transporter SiSulT in oxlate bound state
ComponentsProbable Sulfate permease
KeywordsMEMBRANE PROTEIN / Transporter
Function / homology
Function and homology information


sulfate import across plasma membrane / sulfate transmembrane transporter activity / membrane
Similarity search - Function
SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily
Similarity search - Domain/homology
OXALATE ION / Probable Sulfate permease
Similarity search - Component
Biological speciesSerendipita indica (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsKhandelwal, N.K. / Kumar, P. / Gupta, M. / Finer-Moore, J. / Stroud, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM024485 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Serendipita indica sulfate transporter SiSulT in oxlate bound state
Authors: Khandelwal, N.K. / Kumar, P. / Gupta, M. / Finer-Moore, J. / Stroud, R.M.
History
DepositionMar 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable Sulfate permease
B: Probable Sulfate permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,6204
Polymers176,4442
Non-polymers1762
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Probable Sulfate permease


Mass: 88222.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serendipita indica (fungus) / Gene: PIIN_00937 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G4T6Y6
#2: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: Sulphate transporter with oxlate / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.20665154 MDa / Experimental value: NO
Source (natural)Organism: Serendipita indica (fungus)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5 / Details: 50 mM Tirs ,300mM Nacl pH7.5- LMNG0.01%+.001%CHS
Buffer component
IDConc.NameFormulaBuffer-ID
1300 mMsodium chlorideNaCl1
250 mMTris chlorideTris-Cl1
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sult-0.9mg /ml with +100mM Potassium oxalate monohydrate
Specimen supportDetails: 30 glow 30 hold at 15mA / Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.81 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: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 0.8189 sec. / Electron dose: 47 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10668

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCv4.2.1particle selection
2SerialEMv4.1image acquisitionbeta
4cryoSPARCv4.2.1CTF correction
7PHENIX1.21_5207-000model fitting
9cryoSPARCv4.2.1initial Euler assignment
10cryoSPARCv4.2.1final Euler assignment
11cryoSPARCv4.2.1classification
12cryoSPARCv4.2.13D reconstruction
13PHENIX1.21_5207-000model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 5967145
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 376034 / Symmetry type: POINT
Atomic model buildingB value: 89.8 / Protocol: AB INITIO MODEL / Details: 1:1
Atomic model buildingPDB-ID: 9NF7

9nf7


Pdb chain-ID: A / Accession code: 9NF7 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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