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- PDB-9w99: Structure of betaine-bound state of the human betaine/GABA transp... -

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Basic information

Entry
Database: PDB / ID: 9w99
TitleStructure of betaine-bound state of the human betaine/GABA transporter 1
ComponentsGFP,Maltose/maltodextrin-binding periplasmic protein,Sodium- and chloride-dependent betaine transporter
KeywordsMEMBRANE PROTEIN / TRANSPORT 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
TRIMETHYL GLYCINE / Maltose/maltodextrin-binding periplasmic protein / Sodium- and chloride-dependent betaine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsWu, J.X. / Zhou, J.
Funding support China, 1items
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: Zhou, J. / Liu, J. / Jin, Y. / Wang, Q. / Yu, H. / Wu, J.X.
History
DepositionAug 9, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GFP,Maltose/maltodextrin-binding periplasmic protein,Sodium- and chloride-dependent betaine transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,6195
Polymers144,4201
Non-polymers2004
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein GFP,Maltose/maltodextrin-binding periplasmic protein,Sodium- and chloride-dependent betaine transporter / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / BGT-1 / Na(+)/Cl(-) ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / BGT-1 / Na(+)/Cl(-) betaine/GABA transporter / Solute carrier family 6 member 12


Mass: 144419.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli K-12 (bacteria)
Strain: K-12 / Gene: malE, b4034, JW3994, SLC6A12, BGT1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: P48065
#2: Chemical ChemComp-BET / TRIMETHYL GLYCINE


Mass: 118.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12NO2 / 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestY
Has protein modificationY

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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: BGT1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: TFS KRIOS
Details: Data were collected using a FEI Titan Krios G3 microscope.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5845model refinement
13Coot3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162073 / Symmetry type: POINT
Atomic model buildingDetails: P48065 / Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.04 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024506
ELECTRON MICROSCOPYf_angle_d0.4376138
ELECTRON MICROSCOPYf_dihedral_angle_d10.2061557
ELECTRON MICROSCOPYf_chiral_restr0.037678
ELECTRON MICROSCOPYf_plane_restr0.004748

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