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- PDB-8opq: Structure of Human Solute Carrier 26 family member A6 (SLC26A6) a... -

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Basic information

Entry
Database: PDB / ID: 8opq
TitleStructure of Human Solute Carrier 26 family member A6 (SLC26A6) anion transporter in an inward-facing state
ComponentsSolute carrier family 26 member 6
KeywordsMEMBRANE PROTEIN / Homodimer / Transporter / Exchanger / Bicarbonate / Chloride / Oxalate MEMBRANE PROTEIN
Function / homology
Function and homology information


sulfate:bicarbonate antiporter activity / formate transport / mannitol transmembrane transport / oxalate transport / formate transmembrane transporter activity / Multifunctional anion exchangers / oxalic acid secretion / sulfate transport / protein kinase C signaling / transepithelial chloride transport ...sulfate:bicarbonate antiporter activity / formate transport / mannitol transmembrane transport / oxalate transport / formate transmembrane transporter activity / Multifunctional anion exchangers / oxalic acid secretion / sulfate transport / protein kinase C signaling / transepithelial chloride transport / epithelial fluid transport / sulfate transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / intracellular pH elevation / cellular response to fructose stimulus / chloride:bicarbonate antiporter activity / solute:inorganic anion antiporter activity / vesicle membrane / transepithelial transport / bicarbonate transport / bicarbonate transmembrane transporter activity / intestinal absorption / 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 / PDZ domain binding / angiotensin-activated signaling pathway / brush border membrane / regulation of intracellular pH / 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
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsTippett, D.N. / Breen, C. / Butler, S.J. / Sawicka, M. / Dutzler, R.
Funding support Switzerland, 1items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Solute carrier family 26 member 6
B: Solute carrier family 26 member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,6964
Polymers167,6252
Non-polymers712
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Solute carrier family 26 member 6 / Anion exchange transporter / Pendrin-like protein 1 / Pendrin-L1


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 ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: Homodimer of the human SLC26A6 anion transporter / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Plasmid: pcDXC3VMS
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMSodium ChlorideNaClSodium chloride1
210 mMHEPESC8H18N2O4S1
30.172 mMGDNC56H92O251
SpecimenConc.: 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 supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 67 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 11962

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.2particle selection
2PHENIX1.20.1_4487:model refinement
3EPU2.9image acquisition
5cryoSPARC3.2CTF correction
10cryoSPARC3.2initial Euler assignment
11cryoSPARC4final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1749907
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93169 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210210
ELECTRON MICROSCOPYf_angle_d0.45113884
ELECTRON MICROSCOPYf_dihedral_angle_d10.8423648
ELECTRON MICROSCOPYf_chiral_restr0.0381668
ELECTRON MICROSCOPYf_plane_restr0.0041726

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