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Yorodumi- EMDB-17085: Structure of Human Solute Carrier 26 family member A6 (SLC26A6) a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17085 | |||||||||
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Title | Structure of Human Solute Carrier 26 family member A6 (SLC26A6) anion transporter in an inward-facing state | |||||||||
Map data | Final cryo-EM density map of human SLC26A6 | |||||||||
Sample |
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Keywords | Homodimer / Transporter / Exchanger / Bicarbonate / Chloride / Oxalate MEMBRANE PROTEIN / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information sulfate:bicarbonate antiporter activity / formate transport / formate transmembrane transporter activity / mannitol transmembrane transport / oxalate transport / Multifunctional anion exchangers / oxalic acid secretion / sulfate transport / protein kinase C signaling / transepithelial chloride transport ...sulfate:bicarbonate antiporter activity / formate transport / formate transmembrane transporter activity / mannitol transmembrane transport / oxalate transport / Multifunctional anion exchangers / oxalic acid secretion / sulfate transport / protein kinase C signaling / transepithelial chloride transport / oxalate transmembrane transporter activity / sulfate transmembrane transporter activity / epithelial fluid transport / secondary active sulfate transmembrane transporter activity / intracellular pH elevation / cellular response to fructose stimulus / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / vesicle membrane / bicarbonate transmembrane transporter activity / bicarbonate transport / transepithelial transport / intestinal absorption / chloride transmembrane transporter activity / chloride transport / sperm capacitation / chloride channel activity / efflux transmembrane transporter activity / chloride channel complex / estrous cycle / monoatomic ion transport / cellular response to cAMP / sperm midpiece / positive regulation of dipeptide transmembrane transport / PDZ domain binding / establishment of localization in cell / angiotensin-activated signaling pathway / regulation of intracellular pH / brush border membrane / cytoplasmic vesicle membrane / cellular response to type II interferon / transferase activity / basolateral plasma membrane / vesicle / apical plasma membrane / endoplasmic reticulum / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.28 Å | |||||||||
Authors | Tippett DN / Breen C / Butler SJ / Sawicka M / Dutzler R | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17085.map.gz | 277.6 MB | EMDB map data format | |
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Header (meta data) | emd-17085-v30.xml emd-17085.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17085_fsc.xml | 14.3 KB | Display | FSC data file |
Images | emd_17085.png | 122.3 KB | ||
Masks | emd_17085_msk_1.map | 307.5 MB | Mask map | |
Others | emd_17085_half_map_1.map.gz emd_17085_half_map_2.map.gz | 284.8 MB 284.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17085 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17085 | HTTPS FTP |
-Related structure data
Related structure data | 8opqMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17085.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Final cryo-EM density map of human SLC26A6 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.651 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17085_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half-map 2 of human SLC26A6
File | emd_17085_half_map_1.map | ||||||||||||
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Annotation | Half-map 2 of human SLC26A6 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1 of human SLC26A6
File | emd_17085_half_map_2.map | ||||||||||||
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Annotation | Half-map 1 of human SLC26A6 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homodimer of the human SLC26A6 anion transporter
Entire | Name: Homodimer of the human SLC26A6 anion transporter |
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Components |
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-Supramolecule #1: Homodimer of the human SLC26A6 anion transporter
Supramolecule | Name: Homodimer of the human SLC26A6 anion transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Solute carrier family 26 member 6
Macromolecule | Name: Solute carrier family 26 member 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 83.812328 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE | ||||||||||||
Details | Full-lengthed Human SLC26A6 expressed in HEK293S GNTi- cells |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 11962 / Average electron dose: 67.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |