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- PDB-8ybr: Choline transporter BetT -

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Basic information

Entry
Database: PDB / ID: 8ybr
TitleCholine transporter BetT
ComponentsBCCT family transporter
KeywordsCHOLINE-BINDING PROTEIN / choline transporter
Function / homology:
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsYang, T.J. / Nian, Y.W. / Lin, H.J. / Li, J. / Zhang, J.R. / Fan, M.R.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BCCT family transporter
B: BCCT family transporter
C: BCCT family transporter


Theoretical massNumber of molelcules
Total (without water)225,7643
Polymers225,7643
Non-polymers00
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 BCCT family transporter / Choline transporter BetT


Mass: 75254.680 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: EIZ61_06110 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S3V5U4

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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: Choline transporter BetT / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas syringae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 310945 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00515597
ELECTRON MICROSCOPYf_angle_d0.62321264
ELECTRON MICROSCOPYf_dihedral_angle_d10.7678850
ELECTRON MICROSCOPYf_chiral_restr0.0432370
ELECTRON MICROSCOPYf_plane_restr0.0052664

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