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

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9lnm
Titlehuman Betaine/GABA transporter 1 in complex with GABA
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 / monocarboxylic acid transport / glycine betaine 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 / monocarboxylic acid transport / glycine betaine 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 / sodium ion transmembrane transport / cell projection / 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
GAMMA-AMINO-BUTANOIC ACID / CHOLESTEROL HEMISUCCINATE / Sodium- and chloride-dependent betaine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.67 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. / Hao, K.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,5978
Polymers69,4161
Non-polymers1,1817
Water905
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.: 2 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter, inhibitor*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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 GABA / 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 recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1160GATAN K3 (6k x 4k)
21
31
41
51
61

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Processing

EM softwareName: PHENIX / Category: model refinement
Image processing
IDImage recording-ID
11
22
33
44
55
66
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING ONLY
22
33
44
55
66
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
12.67FSC 0.143 CUT-OFF14900719LNMPOINT
22.67FSC 0.143 CUT-OFF14900719LNMPOINT
319LNMPOINT
419LNMPOINT
519LNMPOINT
619LNMPOINT
72.6714900729LNMPOINT
829LNMPOINT
929LNMPOINT
1029LNMPOINT
1129LNMPOINT
1229LNMPOINT
132.6714900739LNMPOINT
1439LNMPOINT
1539LNMPOINT
1639LNMPOINT
1739LNMPOINT
1839LNMPOINT
192.6714900749LNMPOINT
2049LNMPOINT
2149LNMPOINT
2249LNMPOINT
2349LNMPOINT
2449LNMPOINT
252.6714900759LNMPOINT
2659LNMPOINT
2759LNMPOINT
2859LNMPOINT
2959LNMPOINT
3059LNMPOINT
312.6714900769LNMPOINT
3269LNMPOINT
3369LNMPOINT
3469LNMPOINT
3569LNMPOINT
3669LNMPOINT
RefinementHighest resolution: 2.67 Å

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