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- EMDB-39121: Choline transporter BetT - CHT bound -

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Basic information

Entry
Database: EMDB / ID: EMD-39121
TitleCholine transporter BetT - CHT bound
Map data
Sample
  • Complex: Choline transporter BetT
    • Protein or peptide: BCCT family transporter
  • Ligand: CHOLINE ION
  • Ligand: water
Keywordscholine transporter / CHOLINE-BINDING PROTEIN
Function / homology:
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsYang TJ / Nian YW / Lin HJ / Li J / Zhang JR / Fan MR
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0630101 China
CitationJournal: Sci Adv / Year: 2024
Title: Structure and mechanism of the osmoregulated choline transporter BetT.
Authors: Tianjiao Yang / Yuwei Nian / Huajian Lin / Jing Li / Xiang Lin / Tianming Li / Ruiying Wang / Longfei Wang / Gwyn A Beattie / Jinru Zhang / Minrui Fan /
Abstract: The choline-glycine betaine pathway plays an important role in bacterial survival in hyperosmotic environments. Osmotic activation of the choline transporter BetT promotes the uptake of external ...The choline-glycine betaine pathway plays an important role in bacterial survival in hyperosmotic environments. Osmotic activation of the choline transporter BetT promotes the uptake of external choline for synthesizing the osmoprotective glycine betaine. Here, we report the cryo-electron microscopy structures of BetT in the apo and choline-bound states. Our structure shows that BetT forms a domain-swapped trimer with the C-terminal domain (CTD) of one protomer interacting with the transmembrane domain (TMD) of a neighboring protomer. The substrate choline is bound within a tryptophan prism at the central part of TMD. Together with functional characterization, our results suggest that in species, including the plant pathogen and the human pathogen , BetT is locked at a low-activity state through CTD-mediated autoinhibition in the absence of osmotic stress, and its hyperosmotic activation involves the release of this autoinhibition.
History
DepositionFeb 16, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39121.png

Downloads & links

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Map

FileDownload / File: emd_39121.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.2110355 - 2.0117717
Average (Standard dev.)0.001278205 (±0.044252314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 309.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39121_msk_1.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 : Choline transporter BetT

EntireName: Choline transporter BetT
Components
  • Complex: Choline transporter BetT
    • Protein or peptide: BCCT family transporter
  • Ligand: CHOLINE ION
  • Ligand: water

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Supramolecule #1: Choline transporter BetT

SupramoleculeName: Choline transporter BetT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas syringae (bacteria)

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Macromolecule #1: BCCT family transporter

MacromoleculeName: BCCT family transporter / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas syringae (bacteria)
Molecular weightTheoretical: 75.25468 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSMSSPSTS SSGTVRMNAP VFYFAASFIL IFGIIVIAFP QASGAWLLAA QNWAANTVGW YYMMVMTLYL VFVVVTALSG FGKIKLGAD HDEPEFSYLS WAGMLFAAGI SITLFFFCVS EPLTHLLQPP QGEGGTAEAA RQGMQLLFLH WGLHGWGVFA F VGMALAYF ...String:
MGSMSSPSTS SSGTVRMNAP VFYFAASFIL IFGIIVIAFP QASGAWLLAA QNWAANTVGW YYMMVMTLYL VFVVVTALSG FGKIKLGAD HDEPEFSYLS WAGMLFAAGI SITLFFFCVS EPLTHLLQPP QGEGGTAEAA RQGMQLLFLH WGLHGWGVFA F VGMALAYF AYRHNLPLAL RSALYPLIGK RINGPIGYAV DGFGIIATIF GLGADMGFGV LHLNSGLDYL FGVPHTQWIQ VG LITLMMG AAILVAIAGV DKGVRVMSDI NMLLACALLL FVLFAGPTQH LLNTLVQNIG DYLGALPSKS FDVYAYNKPS DWL GGWTVF YWAWWIAWAP FVGLFIARIS RGRTIREFVF GVLLIPLGFT LAWMSIFGNS AIDQVLNHGM AALGQSAIDD PSMT LYLLL ETYPWSKTVI AVTVFISFVF FVTSADSGTV VLSTLSAKGG NPDEDGPKWL RVFWGVATAL ITSGLLFSGS IDALK SAVV LTSLPFSLIL LLMMWGLHKA FVMESQRQIA QLYSLAPVSG SRRGGWRQRL SQAVHYPSRD EVYRFLDQTV RPAIDE VTA VFVEKGLNVV NVPDPSNDSV TLEIGHGEER PFIYQVQMKG FFTPSFARGG MGSKQLNNRR YYRAEVHLSE GSQDYDL VG YTKEQVINDV LDQYERHMQF LHLVRGSGSG SGSGSWSHPQ FEK

UniProtKB: UNIPROTKB: A0A2S3V5U4

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Macromolecule #2: CHOLINE ION

MacromoleculeName: CHOLINE ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: CHT
Molecular weightTheoretical: 104.171 Da
Chemical component information

ChemComp-CHT:
CHOLINE ION

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 66 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 6
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (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: DIFFRACTION / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 182432
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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