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- PDB-9vbn: Choline transporter BetT with C-terminal 18-amino acid deletion -

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Basic information

Entry
Database: PDB / ID: 9vbn
TitleCholine transporter BetT with C-terminal 18-amino acid deletion
ComponentsHigh-affinity choline transport protein
KeywordsCHOLINE-BINDING PROTEIN / Choline transporter / Membrane Protein / Osmosensory 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
CHOLINE ION / High-affinity choline transport protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsShi, D.J. / Cheng, X.Q. / Jiang, W.X. / Xing, Q.
Funding support China, 2items
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, D.J. / Cheng, X.Q. / Jiang, W.X. / Xing, Q.
History
DepositionJun 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 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

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Assembly

Deposited unit
A: High-affinity choline transport protein
B: High-affinity choline transport protein
C: High-affinity choline transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,6946
Polymers167,3823
Non-polymers3133
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein High-affinity choline transport protein


Mass: 55793.973 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: betT, b0314, JW0306 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABC9
#2: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H14NO / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Homotrimer of choline transporter BetT / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104881 / Symmetry type: POINT

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