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- EMDB-17085: Structure of Human Solute Carrier 26 family member A6 (SLC26A6) a... -

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Basic information

Entry
Database: EMDB / ID: EMD-17085
TitleStructure of Human Solute Carrier 26 family member A6 (SLC26A6) anion transporter in an inward-facing state
Map dataFinal cryo-EM density map of human SLC26A6
Sample
  • Complex: Homodimer of the human SLC26A6 anion transporter
    • Protein or peptide: Solute carrier family 26 member 6
  • Ligand: CHLORIDE ION
KeywordsHomodimer / Transporter / Exchanger / Bicarbonate / Chloride / Oxalate MEMBRANE PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


sulfate:bicarbonate antiporter activity / mannitol transmembrane transport / formate transport / oxalate transport / oxalic acid secretion / formate transmembrane transporter activity / protein kinase C signaling / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity ...sulfate:bicarbonate antiporter activity / mannitol transmembrane transport / formate transport / oxalate transport / oxalic acid secretion / formate transmembrane transporter activity / protein kinase C signaling / Inorganic anion exchange by SLC26 transporters / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / transepithelial chloride transport / epithelial fluid transport / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / intracellular pH elevation / cellular response to fructose stimulus / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / transepithelial transport / bicarbonate transport / bicarbonate transmembrane transporter activity / vesicle membrane / chloride transport / chloride transmembrane transporter activity / intestinal absorption / sperm capacitation / chloride channel activity / efflux transmembrane transporter activity / chloride channel complex / estrous cycle / monoatomic ion transport / sperm midpiece / positive regulation of dipeptide transmembrane transport / cytoplasmic vesicle membrane / chloride transmembrane transport / cellular response to cAMP / angiotensin-activated signaling pathway / regulation of intracellular pH / PDZ domain binding / establishment of localization in cell / brush border membrane / cellular response to type II interferon / transferase activity / basolateral plasma membrane / vesicle / apical plasma membrane / endoplasmic reticulum / identical protein binding / membrane / plasma membrane / cytosol
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
Solute carrier family 26 member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsTippett DN / Breen C / Butler SJ / Sawicka M / Dutzler R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Elife / Year: 2023
Title: Structural and functional properties of the transporter SLC26A6 reveal mechanism of coupled anion exchange.
Authors: David N Tippett / Colum Breen / Stephen J Butler / Marta Sawicka / Raimund Dutzler /
Abstract: Members of the SLC26 family constitute a conserved class of anion transport proteins, which encompasses uncoupled transporters with channel-like properties, coupled exchangers and motor proteins. ...Members of the SLC26 family constitute a conserved class of anion transport proteins, which encompasses uncoupled transporters with channel-like properties, coupled exchangers and motor proteins. Among the 10 functional paralogs in humans, several participate in the secretion of bicarbonate in exchange with chloride and thus play an important role in maintaining pH homeostasis. Previously, we have elucidated the structure of murine SLC26A9 and defined its function as an uncoupled chloride transporter (Walter et al., 2019). Here we have determined the structure of the closely related human transporter SLC26A6 and characterized it as a coupled exchanger of chloride with bicarbonate and presumably also oxalate. The structure defines an inward-facing conformation of the protein that generally resembles known structures of SLC26A9. The altered anion selectivity between both paralogs is a consequence of a remodeled ion binding site located in the center of a mobile unit of the membrane-inserted domain, which also accounts for differences in the coupling mechanism.
History
DepositionApr 7, 2023-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17085.png

Downloads & links

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Map

FileDownload / File: emd_17085.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal cryo-EM density map of human SLC26A6
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.65 Å/pix.
x 432 pix.
= 281.232 Å		0.65 Å/pix.
x 432 pix.
= 281.232 Å		0.65 Å/pix.
x 432 pix.
= 281.232 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.651 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0444
Minimum - Maximum-0.031957947 - 1.9056891
Average (Standard dev.)0.0011954558 (±0.023843175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 281.232 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17085_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 of human SLC26A6

Fileemd_17085_half_map_1.map
AnnotationHalf-map 2 of human SLC26A6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 of human SLC26A6

Fileemd_17085_half_map_2.map
AnnotationHalf-map 1 of human SLC26A6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homodimer of the human SLC26A6 anion transporter

EntireName: Homodimer of the human SLC26A6 anion transporter
Components
  • Complex: Homodimer of the human SLC26A6 anion transporter
    • Protein or peptide: Solute carrier family 26 member 6
  • Ligand: CHLORIDE ION

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Supramolecule #1: Homodimer of the human SLC26A6 anion transporter

SupramoleculeName: Homodimer of the human SLC26A6 anion transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 26 member 6

MacromoleculeName: Solute carrier family 26 member 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.812328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGLADASGP RDTQALLSAT QAMDLRRRDY HMERPLLNQE HLEELGRWGS APRTHQWRTW LQCSRARAYA LLLQHLPVLV WLPRYPVRD WLLGDLLSGL SVAIMQLPQG LAYALLAGLP PVFGLYSSFY PVFIYFLFGT SRHISVGTFA VMSVMVGSVT E SLAPQALN ...String:
MSGLADASGP RDTQALLSAT QAMDLRRRDY HMERPLLNQE HLEELGRWGS APRTHQWRTW LQCSRARAYA LLLQHLPVLV WLPRYPVRD WLLGDLLSGL SVAIMQLPQG LAYALLAGLP PVFGLYSSFY PVFIYFLFGT SRHISVGTFA VMSVMVGSVT E SLAPQALN DSMINETARD AARVQVASTL SVLVGLFQVG LGLIHFGFVV TYLSEPLVRG YTTAAAVQVF VSQLKYVFGL HL SSHSGPL SLIYTVLEVC WKLPQSKVGT VVTAAVAGVV LVVVKLLNDK LQQQLPMPIP GELLTLIGAT GISYGMGLKH RFE VDVVGN IPAGLVPPVA PNTQLFSKLV GSAFTIAVVG FAIAISLGKI FALRHGYRVD SNQELVALGL SNLIGGIFQC FPVS CSMSR SLVQESTGGN SQVAGAISSL FILLIIVKLG ELFHDLPKAV LAAIIIVNLK GMLRQLSDMR SLWKANRADL LIWLV TFTA TILLNLDLGL VVAVIFSLLL VVVRTQMPHY SVLGQVPDTD IYRDVAEYSE AKEVRGVKVF RSSATVYFAN AEFYSD ALK QRCGVDVDFL ISQKKKLLKK QEQLKLKQLQ KEEKLRKQAA SPKGASVSIN VNTSLEDMRS NNVEDCKMMV SSGDKME DA TANGQEDSKA PDGSTLKALG LPQPDFHSLI LDLGALSFVD TVCLKSLKNI FHDFREIEVE VYMAACHSPV VSQLEAGH F FDASITKKHL FASVHDAVTF ALQHPRPVPD SPVSVTRLAL EVLFQ

UniProtKB: Solute carrier family 26 member 6

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Macromolecule #2: CHLORIDE ION

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

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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

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
200.0 mMNaClSodium Chloride
10.0 mMC8H18N2O4SHEPES
0.172 mMC56H92O25GDN
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE
DetailsFull-lengthed Human SLC26A6 expressed in HEK293S GNTi- cells

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 11962 / Average electron dose: 67.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1749907
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93169
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.0)
FSC plot (resolution estimation)

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