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TitleStructure and Inhibition of the Human Na/H Exchanger SLC9B2.
Journal, issue, pagesInt J Mol Sci, Vol. 26, Issue 9, Year 2025
Publish dateApr 29, 2025
AuthorsSukkyeong Jung / Surabhi Kokane / Hang Li / So Iwata / Norimichi Nomura / David Drew /
PubMed AbstractThe sodium/proton exchanger NHA2, also known as SLC9B2, is important for insulin secretion, renal blood pressure regulation, and electrolyte retention. Recent structures of bison NHA2 has revealed ...The sodium/proton exchanger NHA2, also known as SLC9B2, is important for insulin secretion, renal blood pressure regulation, and electrolyte retention. Recent structures of bison NHA2 has revealed its unique 14-transmembrane helix architecture, which is different from SLC9A/NHE members made up from 13-TM helices. Sodium/proton exchangers are functional homodimers, and the additional N-terminal helix in NHA2 was found to alter homodimer assembly. Here, we present the cryo-electron microscopy structures of apo human NHA2 in complex with a Fab fragment and also with the inhibitor phloretin bound at 2.8 and 2.9 Å resolution, respectively. We show how phosphatidic acid (PA) lipids bind to the homodimer interface of NHA2 on the extracellular side, which we propose has a regulatory role linked to cell volume regulation. The ion binding site of human NHA2 has a salt bridge interaction between the ion binding aspartate D278 and R432, an interaction previously broken in the bison NHA2 structure, and these differences suggest a possible ion coupling mechanism. Lastly, the human NHA2 structure in complex with phloretin offers a template for structure-guided drug design, potentially leading to the development of more selective and potent NHA2 inhibitors.
External linksInt J Mol Sci / PubMed:40362458 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 2.9 Å
Structure data

53377

9qub

EMDB-53377, PDB-9qub:
Cryo-EM structure of the human NHA2-Fab complex
Method: EM (single particle) / Resolution: 2.7 Å

53384

9quw

EMDB-53384, PDB-9quw:
Cryo-EM structure of the human NHA2-Fab complex bound to phloretin
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

ChemComp-G50:
3-(4-HYDROXYPHENYL)-1-(2,4,6-TRIHYDROXYPHENYL)PROPAN-1-ONE

Source
  • homo sapiens (human)
  • mus musculus (house mouse)
KeywordsTRANSPORT PROTEIN / Na+/H+ exchanger

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