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- EMDB-52785: Sulfate transporter SLC26A11 in nanodiscs with nanobody Nb4 -

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Basic information

Entry
Database: EMDB / ID: EMD-52785
TitleSulfate transporter SLC26A11 in nanodiscs with nanobody Nb4
Map dataunsharpened map from Cryosparc non-uniform refinement
Sample
  • Complex: SLC26A11 with nanobody Nb4 reconstituted into MSP1-E3D1 nanodiscs together with soyPC
    • Protein or peptide: Sodium-independent sulfate anion transporter
    • Protein or peptide: nanobody Nb4
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: CHLORIDE ION
  • Ligand: water
Keywordssulfate transporter / chloride channel / lysosome / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRasmussen T / Kuhn BT / Bottcher B / Geertsma ER
Funding support Germany, 5 items
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 BT / Geertsma ER / Kovermann P / Bungert-Plumke S / Fahlke C / Haddad BG / Machtens J-P / Rasmussen T / Bottcher B
History
DepositionFeb 11, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52785.png

Downloads & links

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Map

FileDownload / File: emd_52785.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map from Cryosparc non-uniform refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 283.8 Å		0.95 Å/pix.
x 300 pix.
= 283.8 Å		0.95 Å/pix.
x 300 pix.
= 283.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.26715508 - 0.55205554
Average (Standard dev.)0.0007387622 (±0.0134446705)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 283.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: a local resolution filter was applied

Fileemd_52785_additional_1.map
Annotationa local resolution filter was applied
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_52785_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_52785_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SLC26A11 with nanobody Nb4 reconstituted into MSP1-E3D1 nanodiscs...

EntireName: SLC26A11 with nanobody Nb4 reconstituted into MSP1-E3D1 nanodiscs together with soyPC
Components
  • Complex: SLC26A11 with nanobody Nb4 reconstituted into MSP1-E3D1 nanodiscs together with soyPC
    • Protein or peptide: Sodium-independent sulfate anion transporter
    • Protein or peptide: nanobody Nb4
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: SLC26A11 with nanobody Nb4 reconstituted into MSP1-E3D1 nanodiscs...

SupramoleculeName: SLC26A11 with nanobody Nb4 reconstituted into MSP1-E3D1 nanodiscs together with soyPC
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium-independent sulfate anion transporter

MacromoleculeName: Sodium-independent sulfate anion transporter / type: protein_or_peptide / ID: 1
Details: construct without the 23 disordered C-terminal amino acids
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.789668 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPSSVTALGQ ARSSGPGMAP SACCCSPAAL QRRLPILAWL PSYSLQWLKM DFVAGLSVGL TAIPQALAYA EVAGLPPQYG LYSAFMGCF VYFFLGTSRD VTLGPTAIMS LLVSFYTFHE PAYAVLLAFL SGCIQLAMGV LRLGFLLDFI SYPVIKGFTS A AAVTIGFG ...String:
MPSSVTALGQ ARSSGPGMAP SACCCSPAAL QRRLPILAWL PSYSLQWLKM DFVAGLSVGL TAIPQALAYA EVAGLPPQYG LYSAFMGCF VYFFLGTSRD VTLGPTAIMS LLVSFYTFHE PAYAVLLAFL SGCIQLAMGV LRLGFLLDFI SYPVIKGFTS A AAVTIGFG QIKNLLGLQN IPRPFFLQVY HTFLRIAETR VGDAVLGLVC MLLLLVLKLM RDHVPPVHPE MPPGVRLSRG LV WAATTAR NALVVSFAAL VAYSFEVTGY QPFILTGETA EGLPPVRIPP FSVTTANGTI SFTEMVQDMG AGLAVVPLMG LLE SIAVAK AFASQNNYRI DANQELLAIG LTNMLGSLVS SYPVTGSFGR TAVNAQSGVC TPAGGLVTGV LVLLSLDYLT SLFY YIPKS ALAAVIIMAV APLFDTKIFR TLWRVKRLDL LPLCVTFLLC FWEVQYGILA GALVSLLMLL HSAARPETKV SEGPV LVLQ PASGLSFPAM EALREEILSR ALEVSPPRCL VLECTHVCSI DYTVVLGLGE LLQDFQKQGV ALAFVGLQVP VLRVLL SAD LKGFQYFSTL EEAEKHLRQE

UniProtKB: Sodium-independent sulfate anion transporter

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Macromolecule #2: nanobody Nb4

MacromoleculeName: nanobody Nb4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 16.974814 KDa
Recombinant expressionOrganism: Escherichia coli MC1061 (bacteria)
SequenceString:
GSSSQWQLVE SGGGLVQAGD SLRLSCAASG RTFRDYAMGW VRQTPGKERE FVASISSTGA LTFYADSVKG RFTISRDNAK NTVYLQMNI LKPEDTAVYY CARKIPGSSL FLRNKADFDS WGQGTPVTVS AGRAGEQKLI SEEDLNSAVD HHHHHH

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Macromolecule #3: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 3 / Number of copies: 2 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Macromolecule #4: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1 mg/mL
BufferpH: 7.25
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 150 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.4 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: +20 blot force, 5 sec blot time.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 5 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 11086 / Average exposure time: 6.2 sec. / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2147241
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 210771
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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