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

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ID or keywords:

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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 / 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
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

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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)70,6128
Polymers69,4161
Non-polymers1,1967
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, 13 molecules

#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-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4 / 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 recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1160GATAN K3 (6k x 4k)
21
31
41

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Processing

EM softwareName: PHENIX / Category: model refinement
Image processing
IDImage recording-ID
11
22
33
44
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING ONLY
22
33
44
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
12.6FSC 0.143 CUT-OFF31923019LNNPOINT
219LNNPOINT
319LNNPOINT
419LNNPOINT
52.631923019LNNPOINT
619LNNPOINT
719LNNPOINT
819LNNPOINT
92.6FSC 0.143 CUT-OFF31923019LNNPOINT
1019LNNPOINT
1119LNNPOINT
1219LNNPOINT
132.631923019LNNPOINT
1419LNNPOINT
1519LNNPOINT
1619LNNPOINT
172.6FSC 0.143 CUT-OFF31923029LNNPOINT
1829LNNPOINT
1929LNNPOINT
2029LNNPOINT
212.631923029LNNPOINT
2229LNNPOINT
2329LNNPOINT
2429LNNPOINT
252.631923029LNNPOINT
2629LNNPOINT
2729LNNPOINT
2829LNNPOINT
292.631923029LNNPOINT
3029LNNPOINT
3129LNNPOINT
3229LNNPOINT
332.6FSC 0.143 CUT-OFF31923039LNNPOINT
3439LNNPOINT
3539LNNPOINT
3639LNNPOINT
372.631923039LNNPOINT
3839LNNPOINT
3939LNNPOINT
4039LNNPOINT
412.631923039LNNPOINT
4239LNNPOINT
4339LNNPOINT
4439LNNPOINT
452.631923039LNNPOINT
4639LNNPOINT
4739LNNPOINT
4839LNNPOINT
492.6FSC 0.143 CUT-OFF31923049LNNPOINT
5049LNNPOINT
5149LNNPOINT
5249LNNPOINT
532.631923049LNNPOINT
5449LNNPOINT
5549LNNPOINT
5649LNNPOINT
572.631923049LNNPOINT
5849LNNPOINT
5949LNNPOINT
6049LNNPOINT
612.631923049LNNPOINT
6249LNNPOINT
6349LNNPOINT
6449LNNPOINT
RefinementHighest resolution: 2.6 Å

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