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TitleStructural basis of ClC-3 transporter inhibition by TMEM9 and PtdIns(3,5)P.
Journal, issue, pagesNat Struct Mol Biol, Vol. 32, Issue 10, Page 1972-1979, Year 2025
Publish dateJul 16, 2025
AuthorsMarina Schrecker / Yeeun Son / Rosa Planells-Cases / Sumanta Kar / Viktoriia Vorobeva / Uwe Schulte / Bernd Fakler / Thomas J Jentsch / Richard K Hite /
PubMed AbstractThe trafficking and activity of endosomes relies on the exchange of chloride ions and protons by members of the CLC family of chloride channels and transporters; mutations of the genes encoding these ...The trafficking and activity of endosomes relies on the exchange of chloride ions and protons by members of the CLC family of chloride channels and transporters; mutations of the genes encoding these transporters are associated with numerous diseases. Despite their critical roles, the mechanisms by which CLC transporters are regulated are poorly understood. Here we show that two related accessory β-subunits, TMEM9 and TMEM9B, directly interact with ClC-3, ClC-4 and ClC-5. Cryo-electron microscopy structures reveal that TMEM9 inhibits ClC-3 by sealing the cytosolic entrance to the Cl ion pathway. Unexpectedly, we find that phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P) stabilizes the interaction between TMEM9 and ClC-3 and is required for proper regulation of ClC-3 by TMEM9. Collectively, our findings reveal that TMEM9 and PtdIns(3,5)P collaborate to regulate endosomal ion homeostasis by modulating the activity of ClC-3.
External linksNat Struct Mol Biol / PubMed:40670814 / PubMed Central
MethodsEM (single particle)
Resolution2.54 - 3.16 Å
Structure data

47066

9dnw

EMDB-47066, PDB-9dnw:
Human ClC-3:noTMEM9
Method: EM (single particle) / Resolution: 2.9 Å

47067

9dnx

EMDB-47067, PDB-9dnx:
Human ClC-3:TMEM9, TMEM9 Protomer A and B: Complete
Method: EM (single particle) / Resolution: 2.86 Å

47068

9dny

EMDB-47068: Human ClC-3:TMEM9, TMEM9 Protomer A: No CDTMEM9, Protomer B: No LD, No CD
PDB-9dny: Human ClC-3:TMEM9, TMEM9 Protomer A: No CD TMEM9, Protomer B: No LD, No CD
Method: EM (single particle) / Resolution: 3.01 Å

47069

9dnz

EMDB-47069, PDB-9dnz:
Human ClC-3:TMEM9, TMEM9 Protomer A: Complete, TMEM9 Protomer B: No LD, No CD
Method: EM (single particle) / Resolution: 3.16 Å

47070

9do0

EMDB-47070, PDB-9do0:
Human ClC-3
Method: EM (single particle) / Resolution: 2.54 Å

Chemicals

ChemComp-CL:
Unknown entry

ChemComp-CLR:
CHOLESTEROL

PDB-1a8i:
SPIROHYDANTOIN INHIBITOR OF GLYCOGEN PHOSPHORYLASE

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / Ion channel / lysosomal protein / CLC

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