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- PDB-7ch1: The overall structure of SLC26A9 -

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Basic information

Entry
Database: PDB / ID: 7ch1
TitleThe overall structure of SLC26A9
ComponentsSolute carrier family 26 member 9
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Multifunctional anion exchangers / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity / monoatomic anion transport / chloride transport / chloride transmembrane transporter activity / chloride channel activity / monoatomic ion transport ...Multifunctional anion exchangers / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / solute:inorganic anion antiporter activity / bicarbonate transmembrane transporter activity / monoatomic anion transport / chloride transport / chloride transmembrane transporter activity / chloride channel activity / monoatomic ion transport / chloride transmembrane transport / ATPase binding / endosome membrane / apical plasma membrane / Golgi membrane / endoplasmic reticulum membrane / positive regulation of gene expression / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
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 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsChi, X.M. / Chen, Y. / Li, X.R. / Zhang, Y.Y. / Zhou, Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800628 China
National Natural Science Foundation of China (NSFC)31971123 China
CitationJournal: Cell Discov / Year: 2020
Title: Structural insights into the gating mechanism of human SLC26A9 mediated by its C-terminal sequence.
Authors: Ximin Chi / Xueqin Jin / Yun Chen / Xiaoli Lu / Xinyu Tu / Xiaorong Li / Yuanyuan Zhang / Jianlin Lei / Jing Huang / Zhuo Huang / Qiang Zhou / Xiaojing Pan /
Abstract: The human SLC26 transporter family exhibits various transport characteristics, and family member SLC26A9 performs multiple roles, including acting as Cl/HCO exchangers, Cl channels, and Na ...The human SLC26 transporter family exhibits various transport characteristics, and family member SLC26A9 performs multiple roles, including acting as Cl/HCO exchangers, Cl channels, and Na transporters. Some mutations of SLC26A9 are correlated with abnormalities in respiration and digestion systems. As a potential target colocalizing with CFTR in cystic fibrosis patients, SLC26A9 is of great value in drug development. Here, we present a cryo-EM structure of the human SLC26A9 dimer at 2.6 Å resolution. A segment at the C-terminal end is bound to the entry of the intracellular vestibule of the putative transport pathway, which has been proven by electrophysiological experiments to be a gating modulator. Multiple chloride and sodium ions are resolved in the high-resolution structure, identifying novel ion-binding pockets for the first time. Together, our structure takes important steps in elucidating the structural features and regulatory mechanism of SLC26A9, with potential significance in the treatment of cystic fibrosis.
History
DepositionJul 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Solute carrier family 26 member 9
B: Solute carrier family 26 member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,3228
Polymers174,1342
Non-polymers1886
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12570 Å2
ΔGint-149 kcal/mol
Surface area53900 Å2

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Components

#1: Protein Solute carrier family 26 member 9 / Anion transporter/exchanger protein 9


Mass: 87066.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC26A9 / Production host: Homo sapiens (human) / References: UniProt: Q7LBE3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
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: SLC26A9 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3.0.6 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 624027 / Symmetry type: POINT

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