[English] 日本語
Yorodumi
- EMDB-54346: high-affinity choline transporter in DDM with Na+ and choline -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54346
Titlehigh-affinity choline transporter in DDM with Na+ and choline
Map data
Sample
  • Complex: high-affinity choline transporter in DDM with Na+ and choline
    • Protein or peptide: Solute carrier family 5 (High affinity choline transporter), member 7
  • Ligand: SODIUM ION
  • Ligand: CHOLINE ION
  • Ligand: water
KeywordsCholine transporter / membrane protein
Function / homologycholine:sodium symporter activity / : / acetylcholine biosynthetic process / Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile. / plasma membrane / Solute carrier family 5 (High affinity choline transporter), member 7
Function and homology information
Biological speciesSalimicrobium flavidum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsVilchez-Garcia J / Lopez-Alonso JP / Jiang H / Ubarretxena-Belandia I / Tascon I
Funding support Spain, 1 items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2023-146771NA-I00 Spain
CitationJournal: Sci Adv / Year: 2026
Title: Structural insights into a conserved mechanism of choline translocation through CHT.
Authors: Jesus Vilchez-Garcia / Adrián Martínez-Jiménez / Hanxing Jiang / Miguel Luengo / Borja Ochoa-Lizarralde / Jorge Pedro López-Alonso / Jerónimo Pérez-Lorente / Paola Bartoccioni / Raúl ...Authors: Jesus Vilchez-Garcia / Adrián Martínez-Jiménez / Hanxing Jiang / Miguel Luengo / Borja Ochoa-Lizarralde / Jorge Pedro López-Alonso / Jerónimo Pérez-Lorente / Paola Bartoccioni / Raúl Estévez / Victor Guallar / Ekaitz Errasti-Murugarren / Iban Ubarretxena-Belandia / Igor Tascón /
Abstract: Choline is an essential nutrient critical for cellular homeostasis across all domains of life. In humans, choline uptake in cholinergic neurons for its recycling into acetylcholine is mediated by the ...Choline is an essential nutrient critical for cellular homeostasis across all domains of life. In humans, choline uptake in cholinergic neurons for its recycling into acetylcholine is mediated by the high-affinity Na-dependent transporter SLC5A7 (CHT1). Prokaryotes also depend on choline as an osmo-protectant and as metabolite, raising the possibility that bacteria also have choline transporters akin to CHT1. Here, we identify and characterize a bacterial Na-dependent choline transporter (sfCHT) with high sequence identity to CHT1. Cryo-EM structures of Na- and choline-bound sfCHT reveal a LeuT-fold architecture with Na coordination geometry similar to CHT1. Captured in an inward-facing conformation, in sfCHT choline is found at a site near the cytoplasmic side. Computational analysis and transport assays of sfCHT and CHT1 variants reveal local conformational rearrangements in conserved residues along a defined pathway to the cytosolic site. These findings provide structural and mechanistic insights into intracellular choline transition, suggesting an evolutionarily conserved mechanism between the bacterial and human choline transporters.
History
DepositionJul 10, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54346.png

Downloads & links

-
Map

FileDownload / File: emd_54346.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 320 pix.
= 206.784 Å		0.65 Å/pix.
x 320 pix.
= 206.784 Å		0.65 Å/pix.
x 320 pix.
= 206.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6462 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.126
Minimum - Maximum-0.7020326 - 1.0825824
Average (Standard dev.)0.000884727 (±0.019647462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 206.784 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_54346_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_54346_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_54346_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : high-affinity choline transporter in DDM with Na+ and choline

EntireName: high-affinity choline transporter in DDM with Na+ and choline
Components
  • Complex: high-affinity choline transporter in DDM with Na+ and choline
    • Protein or peptide: Solute carrier family 5 (High affinity choline transporter), member 7
  • Ligand: SODIUM ION
  • Ligand: CHOLINE ION
  • Ligand: water

-
Supramolecule #1: high-affinity choline transporter in DDM with Na+ and choline

SupramoleculeName: high-affinity choline transporter in DDM with Na+ and choline
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Salimicrobium flavidum (bacteria)

-
Macromolecule #1: Solute carrier family 5 (High affinity choline transporter), member 7

MacromoleculeName: Solute carrier family 5 (High affinity choline transporter), member 7
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salimicrobium flavidum (bacteria)
Molecular weightTheoretical: 59.706906 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MQPQPSATPD RKQDNKNKNY EKAGLLGFIG LLLVVAVYVA FTGNDVNWGA LVFMFISYAI IFYIGSVTAG KKSDSASDMM VAGRSMPLW VAMFTMTATW VGGGYIAGTA ETTFASGVVW AQAPWGYGLS LIIGGIFYAR KMRRYEFTTM LDPLEVRFGK K VAGVLYLP ...String:
MQPQPSATPD RKQDNKNKNY EKAGLLGFIG LLLVVAVYVA FTGNDVNWGA LVFMFISYAI IFYIGSVTAG KKSDSASDMM VAGRSMPLW VAMFTMTATW VGGGYIAGTA ETTFASGVVW AQAPWGYGLS LIIGGIFYAR KMRRYEFTTM LDPLEVRFGK K VAGVLYLP ALLGELFWSA AILVALGTTF GLILGLDFTT SIIISAIIAV AYTFVGGMWS VALTDVAQII MIIIGMFLVV PF ALSEVGG LGQAWGAYKE GMAGFTNLLP PLDGWNHPDW GNYYWNWWDY ALLLIFGGIP WQVYFQRVLS AKNEKTAMWL SIA AGFLCI ILAVPAVMIG VAGFSADWAS YGIEGPGAAS EILAYVVNYM SPYLVAIVAL GAIAAAVMSS MDSSILSASS MAAW NIYRP LVKPKANGRD IKRTIRVSII LIGLAATIVA LNIDSVYTLW YLCADLVYCM LFPQLTTALF DKKANTYGAI AGLSV SLFL RLGGGEPALG LPAFLPYPMI EDGVVLFPFR TLAMVSGLLT IIVVSRLTQK SCPPQPLRKL KTEMQDE

UniProtKB: Solute carrier family 5 (High affinity choline transporter), member 7

-
Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

-
Macromolecule #3: CHOLINE ION

MacromoleculeName: CHOLINE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CHT
Molecular weightTheoretical: 104.171 Da
Chemical component information

ChemComp-CHT:
CHOLINE ION

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
0.02 %C24H46O11dodecyl-b-D-maltoside (DDM)
20.0 mMC4H11NO3Tris
100.0 mMNaClsodium chloride
1.0 mMC5H14NOcholine
GridModel: UltrAuFoil R0./1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.035 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Average exposure time: 1.26 sec. / Average electron dose: 59.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / Details: Ab-initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.4) / Number images used: 447418
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.4)
Final 3D classificationNumber classes: 4 / Avg.num./class: 246052 / Software - Name: cryoSPARC (ver. v4.4) / Details: Heterogeneous refinement in cryoSPARC.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Model generated with Model Angelo
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 53.4
Output model

PDB-9rws:
high-affinity choline transporter in DDM with Na+ and choline

+
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