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- PDB-9lnn: human Betaine/GABA transporter 1 in complex with Betaine -

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Basic information

Entry
Database: PDB / ID: 9lnn
Titlehuman Betaine/GABA transporter 1 in complex with Betaine
ComponentsSodium- and chloride-dependent betaine transporter
KeywordsPROTEIN TRANSPORT / transport proteins
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 / amino acid transport / cell projection / sodium ion transmembrane transport / presynapse / basolateral plasma membrane / 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.
Similarity search - Domain/homology
TRIMETHYL GLYCINE / CHOLESTEROL HEMISUCCINATE / Sodium- and chloride-dependent betaine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhao, Y. / Hao, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural basis of transportation mechanism of hBGT1
Authors: Zhao, Y. / Xu, H.
History
DepositionJan 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 2.0Jul 8, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Data processing / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / em_3d_reconstruction / em_admin / em_ctf_correction / em_euler_angle_assignment / em_image_processing / em_image_recording / em_software / em_start_model / entity / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_ls_restr / struct_asym / struct_conf / struct_conn
Item: _em_admin.last_update / _entity.formula_weight ..._em_admin.last_update / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _refine.pdbx_stereochemistry_target_values / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Ligand identity / Provider: author / Type: Coordinate replacement
Revision 1.1Jul 8, 2026Data content type: EM metadata
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Group: Data collection / Data processing ...Data collection / Data processing / Experimental summary / Structure summary
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Category: em_3d_reconstruction / em_admin ...em_3d_reconstruction / em_admin / em_ctf_correction / em_euler_angle_assignment / em_image_processing / em_image_recording / em_software / em_start_model / entity
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Item: _em_admin.last_update / _entity.formula_weight ..._em_admin.last_update / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium- and chloride-dependent betaine transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1257
Polymers69,4161
Non-polymers7096
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sodium- and chloride-dependent betaine transporter / BGT-1 / Na(+)/Cl(-) betaine/GABA transporter / Solute carrier family 6 member 12


Mass: 69415.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A12, BGT1 / Production host: Homo sapiens (human) / References: UniProt: P48065

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Non-polymers , 5 types, 12 molecules

#2: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BET / TRIMETHYL GLYCINE


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

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: structure of BGT1 in complex with betaine / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI MORGAGNI
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
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 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
8PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 319230 / Symmetry type: POINT
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024447
ELECTRON MICROSCOPYf_angle_d0.5016063
ELECTRON MICROSCOPYf_dihedral_angle_d5.501604
ELECTRON MICROSCOPYf_chiral_restr0.036674
ELECTRON MICROSCOPYf_plane_restr0.004733

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