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- PDB-9iar: Sulfate transporter SLC26A11 in nanodiscs with nanobody Nb11 -

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Basic information

Entry
Database: PDB / ID: 9iar
TitleSulfate transporter SLC26A11 in nanodiscs with nanobody Nb11
Components
  • Sodium-independent sulfate anion transporter
  • nanobody Nb11
KeywordsMEMBRANE PROTEIN / sulfate transporter / chloride channel / lysosome
Function / homology
Function and homology information


oxalate transport / Transport and metabolism of PAPS / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / chloride channel activity / monoatomic ion transport ...oxalate transport / Transport and metabolism of PAPS / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / monoatomic anion transmembrane transporter activity / chloride:bicarbonate antiporter activity / chloride channel activity / monoatomic ion transport / chloride transmembrane transport / basolateral plasma membrane / apical plasma membrane / lysosomal membrane / endoplasmic reticulum / Golgi apparatus / extracellular exosome / nucleoplasm / 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
Sodium-independent sulfate anion transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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: to be published
Title: Mechanism for (un)coupled transport in the human lysosomal sulfate transporter SLC26A11
Authors: Kuhn, B.T. / Geertsma, E.R. / Kovermann, P. / Bungert-Plumke, S. / Fahlke, C. / Haddad, B.G. / Machtens, J.-P. / Rasmussen, T. / Bottcher, B.
History
DepositionFeb 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 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
B: Sodium-independent sulfate anion transporter
C: nanobody Nb11
A: Sodium-independent sulfate anion transporter
D: nanobody Nb11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,8368
Polymers157,3234
Non-polymers5134
Water00
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 disordered C-terminal 23 amino acids of the human gene
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC26A11 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q86WA9
#2: Antibody nanobody Nb11


Mass: 15871.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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
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 Nb11 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: 75000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 75 sec. / Electron dose: 79 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2552
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4particle selectionblob picker
2EPU2.12.1image acquisition
4cryoSPARC4.4CTF correction
7Coot0.9.8.93model fitting
9cryoSPARC4.4initial Euler assignment
10cryoSPARC4.4final Euler assignment
12cryoSPARC4.43D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1325543
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48803 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310552
ELECTRON MICROSCOPYf_angle_d0.58614372
ELECTRON MICROSCOPYf_dihedral_angle_d5.6811515
ELECTRON MICROSCOPYf_chiral_restr0.0421696
ELECTRON MICROSCOPYf_plane_restr0.0061802

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