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- PDB-9ias: Sulfate transporter SLC26A11 in nanodiscs with nanobody Nb4 -

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Basic information

Entry
Database: PDB / ID: 9ias
TitleSulfate transporter SLC26A11 in nanodiscs with nanobody Nb4
Components
  • Sodium-independent sulfate anion transporter
  • nanobody Nb4
KeywordsMEMBRANE PROTEIN / sulfate transporter / chloride channel / lysosome
Function / homology
Function and homology information


Transport and metabolism of PAPS / oxalate transport / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / sulfate transmembrane transport / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / chloride channel activity / chloride transmembrane transport ...Transport and metabolism of PAPS / oxalate transport / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / sulfate transmembrane transport / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / chloride channel activity / chloride transmembrane transport / transmembrane transport / basolateral plasma membrane / apical plasma membrane / lysosomal membrane / Golgi apparatus / endoplasmic reticulum / extracellular exosome / membrane / 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
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Sodium-independent sulfate anion transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRasmussen, T. / Kuhn, B.T. / Bottcher, B. / Geertsma, E.R.
Funding support Germany, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)359471283 Germany
German Research Foundation (DFG)456578072 Germany
German Research Foundation (DFG)525040890 Germany
German Research Foundation (DFG)FOR5046 GE 2841/3-1 Germany
German Research Foundation (DFG)FOR5046 GE 2841/2-1 Germany
CitationJournal: Nat Commun / Year: 2026
Title: SLC26A11 is an atypical solute carrier with dual transport-channel function mediating lysosomal sulfate transport.
Authors: Benedikt T Kuhn / Peter Kovermann / Bassam G Haddad / Tim Rasmussen / Tamsanqa T Hove / Stefanie Bungert-Plümke / Bettina Böttcher / Jan-Philipp Machtens / Christoph Fahlke / Eric R Geertsma /
Abstract: Membrane transporters and channels are generally assumed to be based on distinct structural and functional principles. SLC26A11, a solute carrier with high expression levels in the brain, has been ...Membrane transporters and channels are generally assumed to be based on distinct structural and functional principles. SLC26A11, a solute carrier with high expression levels in the brain, has been proposed to function as either an anion transporter or a channel. Here, we resolve this apparent discrepancy by demonstrating that SLC26A11 is a dual-function protein capable of operating as both a sulfate transporter and a chloride channel. By resolving its structure and combining biochemical studies and molecular dynamics simulations, we show that SLC26A11 exhibits all the hallmarks of a secondary transporter. The mechanistic basis for its selective ion transport identifies the protein as the elusive lysosomal sulfate exporter. Additionally, we demonstrate that SLC26A11 exhibits an uncoupled, channel-like chloride conductance gated by proton:sulfate symport. Our finding that the chloride-conducting state arises from the transport cycle may contribute to the development of therapeutic strategies for treating brain edema, and the identification of its role in lysosome sulfate efflux may provide new approaches to study and treat lysosomal storage diseases.
History
DepositionFeb 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium-independent sulfate anion transporter
B: Sodium-independent sulfate anion transporter
C: nanobody Nb4
D: nanobody Nb4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,0888
Polymers159,5294
Non-polymers1,5594
Water1448
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 Sodium-independent sulfate anion transporter / Solute carrier family 26 member 11


Mass: 62789.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: construct without the 23 disordered C-terminal amino acids
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC26A11 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q86WA9
#2: Antibody nanobody Nb4


Mass: 16974.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli MC1061 (bacteria)
#3: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: SLC26A11 with nanobody Nb4 reconstituted into MSP1-E3D1 nanodiscs together with soyPC
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.25
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K / Details: +20 blot force, 5 sec blot time

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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: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6.2 sec. / Electron dose: 70 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11086
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 5 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.4particle selectionblob picker
2EPU3.5image acquisition
4cryoSPARC4.4CTF correction
7Coot0.9.8.93model fitting
9PHENIX1.20.1model refinement
10cryoSPARC4.4initial Euler assignment
11cryoSPARC4.4final Euler assignment
13cryoSPARC4.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2147241
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210771 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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