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- EMDB-63238: human Betaine/GABA transporter 1 in inward facing conformation -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63238
Titlehuman Betaine/GABA transporter 1 in inward facing conformation
Map data
Sample
  • Complex: structure of BGT1 protein
    • Protein or peptide: Sodium- and chloride-dependent betaine transporter
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: CHLORIDE ION
Keywordstransport proteins / PROTEIN TRANSPORT
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
Sodium- and chloride-dependent betaine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM
AuthorsZhao Y / Hao K
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63238.png

Downloads & links

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Map

FileDownload / File: emd_63238.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.438
Minimum - Maximum-2.5299637 - 3.7733831
Average (Standard dev.)-0.0013439823 (±0.10357058)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63238_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63238_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : structure of BGT1 protein

EntireName: structure of BGT1 protein
Components
  • Complex: structure of BGT1 protein
    • Protein or peptide: Sodium- and chloride-dependent betaine transporter
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: CHLORIDE ION

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Supramolecule #1: structure of BGT1 protein

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

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Macromolecule #1: Sodium- and chloride-dependent betaine transporter

MacromoleculeName: 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: 69.415859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDGKVAVQEC GPPAVSWVPE EGEKLDQEDE DQVKDRGQWT NKMEFVLSVA GEIIGLGNVW RFPYLCYKNG GGAFFIPYFI FFFVCGIPV FFLEVALGQY TSQGSVTAWR KICPLFQGIG LASVVIESYL NVYYIIILAW ALFYLFSSFT SELPWTTCNN F WNTEHCTD ...String:
MDGKVAVQEC GPPAVSWVPE EGEKLDQEDE DQVKDRGQWT NKMEFVLSVA GEIIGLGNVW RFPYLCYKNG GGAFFIPYFI FFFVCGIPV FFLEVALGQY TSQGSVTAWR KICPLFQGIG LASVVIESYL NVYYIIILAW ALFYLFSSFT SELPWTTCNN F WNTEHCTD FLNHSGAGTV TPFENFTSPV MEFWERRVLG ITSGIHDLGS LRWELALCLL LAWVICYFCI WKGVKSTGKV VY FTATFPY LMLVILLIRG VTLPGAYQGI IYYLKPDLFR LKDPQVWMDA GTQIFFSFAI CQGCLTALGS YNKYHNNCYK DCI ALCFLN SATSFVAGFV VFSILGFMSQ EQGVPISEVA ESGPGLAFIA FPKAVTMMPL SQLWSCLFFI MLIFLGLDSQ FVCV ECLVT ASIDMFPRQL RKSGRRELLI LTIAVMCYLI GLFLVTEGGM YIFQLFDYYA SSGICLLFLS LFEVVCISWV YGADR FYDN IEDMIGYRPW PLVKISWLFL TPGLCLATFL FSLSKYTPLK YNNVYVYPPW GYSIGWFLAL SSMVCVPLFV VITLLK TRG PFRKRLRQLI TPDSSLPQPK QHPCLDGSAG RNFGPSPTRE GLIAGEKETH L

UniProtKB: Sodium- and chloride-dependent betaine transporter

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI MORGAGNI
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing #1

Image processing ID1
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Image processing #2

Image processing ID2

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Image processing #3

Image processing ID3

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Image processing #4

Image processing ID4

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Image processing #5

Image processing ID5
Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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