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Yorodumi- PDB-8opq: Structure of Human Solute Carrier 26 family member A6 (SLC26A6) a... -
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-Basic information
Entry | Database: PDB / ID: 8opq | ||||||
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Title | Structure of Human Solute Carrier 26 family member A6 (SLC26A6) anion transporter in an inward-facing state | ||||||
Components | Solute carrier family 26 member 6 | ||||||
Keywords | MEMBRANE PROTEIN / Homodimer / Transporter / Exchanger / Bicarbonate / Chloride / Oxalate 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 / : / 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 / : / protein kinase C signaling / transepithelial chloride transport / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / epithelial fluid transport / intracellular pH elevation / cellular response to fructose stimulus / chloride:bicarbonate antiporter activity / transepithelial transport / solute:inorganic anion antiporter activity / bicarbonate transport / bicarbonate transmembrane transporter activity / intestinal absorption / vesicle membrane / chloride transport / chloride transmembrane transporter activity / 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 / establishment of localization in cell / angiotensin-activated signaling pathway / regulation of intracellular pH / PDZ domain binding / brush border membrane / cytoplasmic vesicle 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å | ||||||
Authors | Tippett, D.N. / Breen, C. / Butler, S.J. / Sawicka, M. / Dutzler, R. | ||||||
Funding support | Switzerland, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8opq.cif.gz | 253.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8opq.ent.gz | 202.1 KB | Display | PDB format |
PDBx/mmJSON format | 8opq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8opq_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8opq_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8opq_validation.xml.gz | 54.9 KB | Display | |
Data in CIF | 8opq_validation.cif.gz | 80.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/8opq ftp://data.pdbj.org/pub/pdb/validation_reports/op/8opq | HTTPS FTP |
-Related structure data
Related structure data | 17085MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 83812.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC26A6 / Plasmid: pcDXC3VMS / Cell line (production host): HEK293S GNTi- / Production host: Homo sapiens (human) / References: UniProt: Q9BXS9 #2: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Homodimer of the human SLC26A6 anion transporter / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Plasmid: pcDXC3VMS | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Full-lengthed Human SLC26A6 expressed in HEK293S GNTi- cells | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 67 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 11962 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1749907 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93169 / Symmetry type: POINT | ||||||||||||||||||||||||||||
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