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- EMDB-64928: Choline transporter BetT with C-terminal 18-amino acid deletion -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64928
TitleCholine transporter BetT with C-terminal 18-amino acid deletion
Map data
Sample
  • Complex: Homotrimer of choline transporter BetT
    • Protein or peptide: High-affinity choline transport protein
  • Ligand: CHOLINE ION
KeywordsCholine transporter / Membrane Protein / Osmosensory Protein / CHOLINE-BINDING PROTEIN
Function / homology
Function and homology information


choline transmembrane transporter activity / : / choline transport / transmembrane transporter activity / DNA damage response / plasma membrane
Similarity search - Function
BCCT transporter, conserved site / BCCT family of transporters signature. / BCCT transporter family / BCCT, betaine/carnitine/choline family transporter
Similarity search - Domain/homology
High-affinity choline transport protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsShi DJ / Cheng XQ / Jiang WX / Xing Q
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371277 China
National Natural Science Foundation of China (NSFC)32301028 China
CitationJournal: To Be Published
Title: Structural and Mechanistic insight into Osmosensation and Osmoregulation by the Bacterial Choline Transporter BetT
Authors: Shi DJ / Cheng XQ / Jiang WX / Xing Q
History
DepositionJun 4, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64928.png

Downloads & links

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Map

FileDownload / File: emd_64928.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 480 pix.
= 272.16 Å		0.57 Å/pix.
x 480 pix.
= 272.16 Å		0.57 Å/pix.
x 480 pix.
= 272.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.567 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07199
Minimum - Maximum-0.6578576 - 0.88481134
Average (Standard dev.)0.00018147231 (±0.019275472)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 272.15997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64928_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_64928_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 : Homotrimer of choline transporter BetT

EntireName: Homotrimer of choline transporter BetT
Components
  • Complex: Homotrimer of choline transporter BetT
    • Protein or peptide: High-affinity choline transport protein
  • Ligand: CHOLINE ION

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Supramolecule #1: Homotrimer of choline transporter BetT

SupramoleculeName: Homotrimer of choline transporter BetT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: High-affinity choline transport protein

MacromoleculeName: High-affinity choline transport protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 55.793973 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: REKDKINPVV FYTSAGLILL FSLTTILFRD FSALWIGRTL DWVSKTFGWY YLLAATLYIV FVVCIACSRF GSVKLGPEQS KPEFSLLSW AAMLFAAGIG IDLMFFSVAE PVTQYMQPPE GAGQTIEAAR QAMVWTLFHY GLTGWSMYAL MGMALGYFSY R YNLPLTIR ...String:
REKDKINPVV FYTSAGLILL FSLTTILFRD FSALWIGRTL DWVSKTFGWY YLLAATLYIV FVVCIACSRF GSVKLGPEQS KPEFSLLSW AAMLFAAGIG IDLMFFSVAE PVTQYMQPPE GAGQTIEAAR QAMVWTLFHY GLTGWSMYAL MGMALGYFSY R YNLPLTIR SALYPIFGKR INGPIGHSVD IAAVIGTIFG IATTLGIGVV QLNYGLSVLF DIPDSMAAKA ALIALSVIIA TI SVTSGVD KGIRVLSELN VALALGLILF VLFMGDTSFL LNALVLNVGD YVNRFMGMTL NSFAFDRPVE WMNNWTLFFW AWW VAWSPF VGLFLARISR GRTIRQFVLG TLIIPFTFTL LWLSVFGNSA LYEIIHGGAA FAEEAMVHPE RGFYSLLAQY PAFT FSASV ATITGLLFYV TSADSGALVL GNFTSQLKDI NSDAPGWLRV FWSVAIGLLT LGMLMTNGIS ALQNTTVIMG LPFSF VIFF VMAGLYKSLK VEDYRRESAN R

UniProtKB: High-affinity choline transport protein

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration12 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104881
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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