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- EMDB-65769: Structure of the apo state of human betaine/GABA transporter 1 in... -

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Basic information

Entry
Database: EMDB / ID: EMD-65769
TitleStructure of the apo state of human betaine/GABA transporter 1 in the inward-facing conformation
Map data
Sample
  • Complex: BGT1
    • Protein or peptide: GFP,Maltose/maltodextrin-binding periplasmic protein,Sodium- and chloride-dependent betaine transporter
  • Ligand: CHLORIDE ION
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


gamma-aminobutyric acid transport / gamma-aminobutyric acid reuptake / Reuptake of GABA / monocarboxylic acid transmembrane transporter activity / glycine betaine transport / monocarboxylic acid transport / Creatine metabolism / gamma-aminobutyric acid:sodium:chloride symporter activity / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity ...gamma-aminobutyric acid transport / gamma-aminobutyric acid reuptake / Reuptake of GABA / monocarboxylic acid transmembrane transporter activity / glycine betaine transport / monocarboxylic acid transport / Creatine metabolism / gamma-aminobutyric acid:sodium:chloride symporter activity / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / SLC-mediated transport of neurotransmitters / detection of maltose stimulus / maltose transport complex / carbohydrate transport / amino acid transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cell projection / ATP-binding cassette (ABC) transporter complex / sodium ion transmembrane transport / cell chemotaxis / outer membrane-bounded periplasmic space / presynapse / basolateral plasma membrane / periplasmic space / DNA damage response / membrane / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter, betaine / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...Sodium:neurotransmitter symporter, betaine / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Sodium- and chloride-dependent betaine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsWu JX / Zhou J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371266 China
CitationJournal: Nat Commun / Year: 2026
Title: Substrate recognition and allosteric inhibition of human betaine/GABA transporter 1.
Authors: Jun Zhou / Jiameng Liu / Yuchen Jin / Qianyu Wang / Haibo Yu / Jing-Xiang Wu /
Abstract: 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 ...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.
History
DepositionAug 9, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65769.png

Downloads & links

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Map

FileDownload / File: emd_65769.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.152 Å		1.07 Å/pix.
x 256 pix.
= 273.152 Å		1.07 Å/pix.
x 256 pix.
= 273.152 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-1.9750975 - 3.3688154
Average (Standard dev.)-0.0010541612 (±0.06183998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.152 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65769_msk_1.map
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Half map: #1

Fileemd_65769_half_map_1.map
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Half map: #2

Fileemd_65769_half_map_2.map
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Sample components

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Entire : BGT1

EntireName: BGT1
Components
  • Complex: BGT1
    • Protein or peptide: GFP,Maltose/maltodextrin-binding periplasmic protein,Sodium- and chloride-dependent betaine transporter
  • Ligand: CHLORIDE ION

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Supramolecule #1: BGT1

SupramoleculeName: BGT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: GFP,Maltose/maltodextrin-binding periplasmic protein,Sodium- and ...

MacromoleculeName: GFP,Maltose/maltodextrin-binding periplasmic protein,Sodium- and chloride-dependent betaine transporter
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 144.419703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATIG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGKYKTR AVVKFEGDTL VNRIELKGTD FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFTVR ...String:
MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATIG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGKYKTR AVVKFEGDTL VNRIELKGTD FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFTVR HNVEGSGHHH HHHHHADRKA AVSHWQQSSG LVPRGSGWSH PQFEKGSGDY KDDDDKGSGW SHPQFEKGSG DG SVQLADH YQQNTPIGDG PVLLPDNHYL STQTKLSKDP NEKRDHMVLH EYVNAAGITG SMKIEEGKLV IWINGDKGYN GLA EVGKKF EKDTGIKVTV EHPDKLEEKF PQVAATGDGP DIIFWAHDRF GGYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNG KLIAY PIAVEALSLI YNKDLLPNPP KTWEEIPALD KELKAKGKSA LMFNLQEPYF TWPLIAADGG YAFKYENGKY DIKDV GVDN AGAKAGLTFL VDLIKNKHMN ADTDYSIAEA AFNKGETAMT INGPWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGV LSA GINAASPNKE LAKEFLENYL LTDEGLEAVN KDKPLGAVAL KSYEEELVKD PRIAATMENA QKGEIMPNIP QMSAFWY AV RTAVINAASG RQTVDEALKD AQTGGLEVLF QGPEFMDGKV AVQERGPPAV SWVPEEGEKL DQEDEDQVKD RGQWTNKM E FVLSVAGEII GLGNVWRFPY LCYKNGGGAF FIPYFIFFFV CGIPVFFLEV ALGQYTSQGS VTAWRKICPL FQGIGLASV VIESYLNVYY IIILAWALFY LFSSFTSELP WTTCNNFWNT EHCTDFLNHS GAGTVTPFEN FTSPVMEFWE RRVLGITSGI HDLGSLRWE LALCLLLAWV ICYFCIWKGV KSTGKVVYFT ATFPYLMLVI LLIRGVTLPG AYQGIIYYLK PDLFRLKDPQ V WMDAGTQI FFSFAICQGC LTALGSYNKY HNNCYKDCIA LCFLNSATSF VAGFVVFSIL GFMSQEQGVP ISEVAESGPG LA FIAFPKA VTMMPLSQLW SCLFFIMLIF LGLDSQFVCV ECLVTASIDM FPRQLRKSGR RELLILTIAV MCYLIGLFLV TEG GMYIFQ LFDYYASSGI CLLFLSLFEV VCISWVYGAD RFYDNIEDMI GYRPWPLVKI SWLFLTPGLC LATFLFSLSK YTPL KYNNV YVYPPWGYSI GWFLALSSMV CVPLFVVITL LKTRGPFRKR LRQLITPDSS LPQPKQHPCL DGSAGRNFGP SPTRE GLIA GEKETHL

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Sodium- and chloride-dependent betaine transporter

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Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
DetailsData were collected using a FEI Titan Krios G3 microscope.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 145802
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: P48065
Output model

PDB-9w9b:
Structure of the apo state of human betaine/GABA transporter 1 in the inward-facing conformation

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