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- PDB-9qu3: Cryo-EM structure of the human choline transporter-like protein h... -

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Basic information

Entry
Database: PDB / ID: 9qu3
TitleCryo-EM structure of the human choline transporter-like protein hCTL1 in LMNG
ComponentsCholine transporter-like protein 1
KeywordsMEMBRANE PROTEIN / SLC44
Function / homology
Function and homology information


ethanolamine transport / ethanolamine transmembrane transporter activity / Choline catabolism / : / choline catabolic process / choline transmembrane transporter activity / choline transport / phosphatidylcholine biosynthetic process / antiporter activity / Synthesis of PC ...ethanolamine transport / ethanolamine transmembrane transporter activity / Choline catabolism / : / choline catabolic process / choline transmembrane transporter activity / choline transport / phosphatidylcholine biosynthetic process / antiporter activity / Synthesis of PC / transport across blood-brain barrier / transmembrane transport / mitochondrial outer membrane / mitochondrion / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Choline transporter-like / Plasma-membrane choline transporter
Similarity search - Domain/homology
Choline transporter-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDriller, J.H. / Nel, L. / Pedersen, B.P.
Funding support Denmark, European Union, 4items
OrganizationGrant numberCountry
LundbeckfondenR380-2021-1207 Denmark
H2020 Marie Curie Actions of the European Commission890822European Union
Danish National Research Foundation0135-00032B Denmark
The Carlsberg FoundationCF19-0127 Denmark
CitationJournal: Life Sci Alliance / Year: 2026
Title: Structural and biochemical comparison of the FLVCR and CTL membrane protein families in eukaryotes.
Authors: Lynette Nel / Jan H Driller / Ronja Driller / Kelly M Frain / Bjørn P Pedersen /
Abstract: The organic cation choline is essential for eukaryotic metabolism. Recently, the feline leukemia virus subgroup C receptor-related (FLVCR, SLC49) family was demonstrated as central for basal choline ...The organic cation choline is essential for eukaryotic metabolism. Recently, the feline leukemia virus subgroup C receptor-related (FLVCR, SLC49) family was demonstrated as central for basal choline transport, questioning the role of the choline transporter-like (CTL, SLC44) family in this capacity. Here, we use oocytes to confirm that FLVCR1 (SLC49A1) and FLVCR2 (SLC49A2) proteins are choline transporters. CTL1 (SLC44A1) does not transport choline under the same conditions, supported by other CTL proteins, CherI and PNS1, which also display no choline transport activity. We present the atomic structures of FLVCR2, CTL1, and PNS1. The 3.4 Å cryo-EM structure of FLVCR2 has choline in the binding pocket. The 3.3 Å cryo-EM structure of CTL1 and the 2.7 Å crystal structure of PNS1 reveal an unusual protein fold, weakly related to the mitochondrial carrier family (SLC25). The unusual fold appears incompatible with transmembrane transport and implies a different and, so far, unknown function for CTL proteins. Our results support FLVCR proteins as choline transporters and suggest a nontransport role for CTL proteins.
History
DepositionApr 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 27, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choline transporter-like protein 1


Theoretical massNumber of molelcules
Total (without water)73,8941
Polymers73,8941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Choline transporter-like protein 1 / CDw92 / Solute carrier family 44 member 1


Mass: 73893.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC44A1, CD92, CDW92, CTL1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WWI5
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: Choline transporter-like protein 1 in LMNG detergent / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115320 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 78.08 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212960
ELECTRON MICROSCOPYf_angle_d0.43354021
ELECTRON MICROSCOPYf_chiral_restr0.0319488
ELECTRON MICROSCOPYf_plane_restr0.0039468
ELECTRON MICROSCOPYf_dihedral_angle_d3.8733385

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