[English] 日本語
Yorodumi
- EMDB-65768: Structure of GABA-bound state of the human betaine/GABA transporter 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65768
TitleStructure of GABA-bound state of the human betaine/GABA transporter 1
Map data
Sample
  • Complex: BGT1
    • Protein or peptide: GFP,Maltose/maltodextrin-binding periplasmic protein,Sodium- and chloride-dependent betaine transporter
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION
KeywordsTRANSPORT PROTEIN / MEMBRANE 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
Maltose/maltodextrin-binding periplasmic protein / Sodium- and chloride-dependent betaine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsWu JX / Zhou J
Funding support China, 1 items
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 JX
History
DepositionAug 9, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_65768.png

Downloads & links

-
Map

FileDownload / File: emd_65768.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.)
1.07 Å/pix.
x 256 pix.
= 273.152 Å		1.07 Å/pix.
x 256 pix.
= 273.152 Å		1.07 Å/pix.
x 256 pix.
= 273.152 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.3964453 - 3.6012707
Average (Standard dev.)-0.0013852422 (±0.06963186)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.152 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_65768_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65768_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65768_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : BGT1

EntireName: BGT1
Components
  • Complex: BGT1
    • Protein or peptide: GFP,Maltose/maltodextrin-binding periplasmic protein,Sodium- and chloride-dependent betaine transporter
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION

-
Supramolecule #1: BGT1

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

-
Macromolecule #1: GFP,Maltose/maltodextrin-binding periplasmic protein,Sodium- and ...

MacromoleculeName: GFP,Maltose/maltodextrin-binding periplasmic protein,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: 144.419703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATIG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGKYKTR AVVKFEGDTL VNRIELKGTD FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFTVR ...String:
MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATIG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGKYKTR AVVKFEGDTL VNRIELKGTD FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFTVR HNVEGSGHHH HHHHHADRKA AVSHWQQSSG LVPRGSGWSH PQFEKGSGDY KDDDDKGSGW SHPQFEKGSG DG SVQLADH YQQNTPIGDG PVLLPDNHYL STQTKLSKDP NEKRDHMVLH EYVNAAGITG SMKIEEGKLV IWINGDKGYN GLA EVGKKF EKDTGIKVTV EHPDKLEEKF PQVAATGDGP DIIFWAHDRF GGYAQSGLLA EITPDKAFQD KLYPFTWDAV RYNG KLIAY PIAVEALSLI YNKDLLPNPP KTWEEIPALD KELKAKGKSA LMFNLQEPYF TWPLIAADGG YAFKYENGKY DIKDV GVDN AGAKAGLTFL VDLIKNKHMN ADTDYSIAEA AFNKGETAMT INGPWAWSNI DTSKVNYGVT VLPTFKGQPS KPFVGV LSA GINAASPNKE LAKEFLENYL LTDEGLEAVN KDKPLGAVAL KSYEEELVKD PRIAATMENA QKGEIMPNIP QMSAFWY AV RTAVINAASG RQTVDEALKD AQTGGLEVLF QGPEFMDGKV AVQERGPPAV SWVPEEGEKL DQEDEDQVKD RGQWTNKM E FVLSVAGEII GLGNVWRFPY LCYKNGGGAF FIPYFIFFFV CGIPVFFLEV ALGQYTSQGS VTAWRKICPL FQGIGLASV VIESYLNVYY IIILAWALFY LFSSFTSELP WTTCNNFWNT EHCTDFLNHS GAGTVTPFEN FTSPVMEFWE RRVLGITSGI HDLGSLRWE LALCLLLAWV ICYFCIWKGV KSTGKVVYFT ATFPYLMLVI LLIRGVTLPG AYQGIIYYLK PDLFRLKDPQ V WMDAGTQI FFSFAICQGC LTALGSYNKY HNNCYKDCIA LCFLNSATSF VAGFVVFSIL GFMSQEQGVP ISEVAESGPG LA FIAFPKA VTMMPLSQLW SCLFFIMLIF LGLDSQFVCV ECLVTASIDM FPRQLRKSGR RELLILTIAV MCYLIGLFLV TEG GMYIFQ LFDYYASSGI CLLFLSLFEV VCISWVYGAD RFYDNIEDMI GYRPWPLVKI SWLFLTPGLC LATFLFSLSK YTPL KYNNV YVYPPWGYSI GWFLALSSMV CVPLFVVITL LKTRGPFRKR LRQLITPDSS LPQPKQHPCL DGSAGRNFGP SPTRE GLIA GEKETHL

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Sodium- and chloride-dependent betaine transporter

-
Macromolecule #2: GAMMA-AMINO-BUTANOIC ACID

MacromoleculeName: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: ABU
Molecular weightTheoretical: 103.12 Da
Chemical component information

ChemComp-ABU:
GAMMA-AMINO-BUTANOIC ACID / neurotransmitter, inhibitor*YM

-
Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

-
Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
DetailsData were collected using a FEI Titan Krios G3 microscope.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 137106
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: P48065
Output model

PDB-9w9a:
Structure of GABA-bound state of the human betaine/GABA transporter 1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more