8R8T | pdb_00008r8t

Cryo-EM structure of the inward-facing ethanolamine-bound FLVCR1

• PDB DOI: https://doi.org/10.2210/pdb8R8T/pdb
• EM Map EMD-19009: EMDB EMDataResource

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


• Deposited: 2023-11-29 Released: 2024-04-17 
• Deposition Author(s): Weng, T.-H., Wu, D., Safarian, S.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Molecular mechanism of choline and ethanolamine transport in humans.

Ri, K., Weng, T.H., Claveras Cabezudo, A., Josting, W., Zhang, Y., Bazzone, A., Leong, N.C.P., Welsch, S., Doty, R.T., Gursu, G., Lim, T.J.Y., Schmidt, S.L., Abkowitz, J.L., Hummer, G., Wu, D., Nguyen, L.N., Safarian, S.

(2024) Nature 630: 501-508

• PubMed: 38778100 
• DOI: https://doi.org/10.1038/s41586-024-07444-7
• Primary Citation of Related Structures:  
  8QCS, 8QCT, 8QCX, 8QCY, 8QD0, 8R8T


• PubMed Abstract: 
  

  Human feline leukaemia virus subgroup C receptor-related proteins 1 and 2 (FLVCR1 and FLVCR2) are members of the major facilitator superfamily ¹ . Their dysfunction is linked to several clinical disorders, including PCARP, HSAN and Fowler syndrome ^2-7 . Earlier studies concluded that FLVCR1 may function as a haem exporter ^8-12 , whereas FLVCR2 was suggested to act as a haem importer ¹³ , yet conclusive biochemical and detailed molecular evidence remained elusive for the function of both transporters ^14-16 . Here, we show that FLVCR1 and FLVCR2 facilitate the transport of choline and ethanolamine across the plasma membrane, using a concentration-driven substrate translocation process. Through structural and computational analyses, we have identified distinct conformational states of FLVCRs and unravelled the coordination chemistry underlying their substrate interactions. Fully conserved tryptophan and tyrosine residues form the binding pocket of both transporters and confer selectivity for choline and ethanolamine through cation-π interactions. Our findings clarify the mechanisms of choline and ethanolamine transport by FLVCR1 and FLVCR2, enhance our comprehension of disease-associated mutations that interfere with these vital processes and shed light on the conformational dynamics of these major facilitator superfamily proteins during the transport cycle.

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Organizational Affiliation: 
• Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
Immunology Program, Life Sciences Institute, National University of Singapore, Singapore, Singapore.
Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore.
Cardiovascular Disease Research (CVD) Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
Department and Emeritus Group of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany.
IMPRS on Cellular Biophysics, Frankfurt, Germany.
Nanion Technologies GmbH, Munich, Germany.
Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt, Germany.
Division of Hematology, Department of Medicine, University of Washington, Seattle, WA, USA.
Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany. [e-mail].
Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany. [e-mail].
Department and Emeritus Group of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany. [e-mail].
Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt, Germany. [e-mail].
Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. [e-mail].
Immunology Program, Life Sciences Institute, National University of Singapore, Singapore, Singapore. [e-mail].
Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, Singapore. [e-mail].
Cardiovascular Disease Research (CVD) Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. [e-mail].
Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. [e-mail].
Department and Emeritus Group of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany. [e-mail].
Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt, Germany. [e-mail].
Institute of Clinical Pharmacology, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany. [e-mail].
Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Frankfurt, Germany. [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: 60.96 kDa 
• Atom Count: 3,256 
• Modeled Residue Count: 418 
• Deposited Residue Count: 563 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme transporter FLVCR1	A	563	Homo sapiens	Mutation(s): 0  Gene Names: FLVCR1, FLVCR Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5Y0 (Homo sapiens) Explore Q9Y5Y0  Go to UniProtKB:  Q9Y5Y0
PHAROS:  Q9Y5Y0 GTEx:  ENSG00000162769

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ETA (Subject of Investigation/LOI)	B [auth A]	ETHANOLAMINE C2 H7 N O HZAXFHJVJLSVMW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Weng, T.-H., Wu, D., Safarian, S.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Database references
• Version 1.2: 2024-06-05
  Changes: Database references
• Version 1.3: 2024-06-19
  Changes: Database references