9QU4 | pdb_00009qu4

Cryo-EM structure of the inward-open choline-bound state of choline/ethanolamine transporter FLVCR2

• PDB DOI: https://doi.org/10.2210/pdb9QU4/pdb
• EM Map EMD-53371: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2025-04-10 Released: 2025-06-11 
• Deposition Author(s): Driller, J.H., Nel, L., Pedersen, B.P.
• Funding Organization(s): Lundbeckfonden, H2020 Marie Curie Actions of the European Commission, Danish Council for Independent Research, The Carlsberg Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural and biochemical comparison of the FLVCR and CTL membrane protein families in eukaryotes.

Nel, L., Driller, J.H., Driller, R., Frain, K.M., Pedersen, B.P.

(2026) Life Sci Alliance 9

• PubMed: 42114998 
• DOI: https://doi.org/10.26508/lsa.202503583
• Primary Citation Related Structures: 
  9F63, 9QU3, 9QU4


• PubMed 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 transport, questioning the role of the choline transporter-like (CTL, SLC44) family in this capacity. Here, we use Xenopus laevis 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, Arabidopsis thaliana CherI and Saccharomyces cerevisiae 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.

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Organizational Affiliation: 
• Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 66.47 kDa 
• Atom Count: 3,137 
• Modeled Residue Count: 402 
• Deposited Residue Count: 597 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin G-binding protein A,Choline/ethanolamine transporter FLVCR2	A	597	Homo sapiens	Mutation(s): 0  Gene Names: spa, FLVCR2, C14orf58 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P02976  Go to UniProtKB:  P02976
Find proteins for Q9UPI3 (Homo sapiens) Explore Q9UPI3  Go to UniProtKB:  Q9UPI3
PHAROS:  Q9UPI3 GTEx:  ENSG00000119686
UniProt Groups	Q9UPI3P02976

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CHT (Subject of Investigation/LOI)	B [auth A]	CHOLINE ION C5 H14 N O OEYIOHPDSNJKLS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Driller, J.H., Nel, L., Pedersen, B.P.

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Funding Organization	Location	Grant Number
Lundbeckfonden	Denmark	R380-2021-1207
H2020 Marie Curie Actions of the European Commission	European Union	890822
Danish Council for Independent Research	Denmark	0135-00032B
The Carlsberg Foundation	Denmark	CF19-0127

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release
  
• Version 1.1: 2026-05-27
  Changes: Data collection, Database references