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TitleSubstrate recognition and allosteric inhibition of human betaine/GABA transporter 1.
Journal, issue, pagesNat Commun, Year 2026
Publish dateMay 19, 2026
AuthorsJun Zhou / Jiameng Liu / Yuchen Jin / Qianyu Wang / Haibo Yu / Jing-Xiang Wu /
PubMed AbstractThe betaine/GABA transporter 1 (BGT1, SLC6A12) regulates neurotransmitter clearance and osmotic balance by transporting GABA and betaine in a sodium- and chloride-dependent manner. BGT1 has become a ...The betaine/GABA transporter 1 (BGT1, SLC6A12) regulates neurotransmitter clearance and osmotic balance by transporting GABA and betaine in a sodium- and chloride-dependent manner. BGT1 has become a promising target for epilepsy treatment due to the anticonvulsant effects observed with BGT1 inhibitors. Although BGT1 plays key roles in both renal and neuronal physiology, the molecular basis of its substrate recognition and inhibition remains unclear. Here, we report cryo-EM structures of human BGT1 in the apo form and in complex with GABA, betaine, the substrate-like inhibitor ATPCA, and the selective inhibitor BPDBA all without the use of fiducial markers. These structures capture BGT1 in both occluded and inward-facing conformations, delineating the conformational transitions associated with substrate release. BPDBA binds to an intracellular cavity adjacent to the intracellular gate. This binding mode locks TM1a to transit and inhibits substrate release. Together, our results uncover distinct mechanisms of substrate recognition and allosteric inhibition of hBGT1, offering structural insights for the development of hBGT1-selective modulators.
External linksNat Commun / PubMed:42156742
MethodsEM (single particle)
Resolution2.71 - 3.04 Å
Structure data

65765

9w97

EMDB-65765, PDB-9w97:
Structure of BPDBA-bound state of the human betaine/GABA transporter 1
Method: EM (single particle) / Resolution: 2.84 Å

65766

9w98

EMDB-65766, PDB-9w98:
Structure of ATPCA-bound state of the human betaine/GABA transporter 1
Method: EM (single particle) / Resolution: 2.71 Å

65767

9w99

EMDB-65767, PDB-9w99:
Structure of betaine-bound state of the human betaine/GABA transporter 1
Method: EM (single particle) / Resolution: 3.04 Å

65768

9w9a

EMDB-65768, PDB-9w9a:
Structure of GABA-bound state of the human betaine/GABA transporter 1
Method: EM (single particle) / Resolution: 2.98 Å

65769

9w9b

EMDB-65769, PDB-9w9b:
Structure of the apo state of human betaine/GABA transporter 1 in the inward-facing conformation
Method: EM (single particle) / Resolution: 2.87 Å

65770

9w9c

EMDB-65770, PDB-9w9c:
Structure of the apo state of human betaine/GABA transporter 1 in the occluded conformation
Method: EM (single particle) / Resolution: 3.02 Å

Chemicals

PDB-1evn:
NMR OBSERVATION OF A-TETRAD

ChemComp-CL:
Unknown entry

PDB-1emk:
GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT

ChemComp-NA:
Unknown entry

ChemComp-BET:
TRIMETHYL GLYCINE

ChemComp-ABU:
GAMMA-AMINO-BUTANOIC ACID / neurotransmitter, inhibitor*YM

Source
  • homo sapiens (human)
  • escherichia coli k-12 (bacteria)
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN

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