7TX6

Cryo-EM structure of the human reduced folate carrier in complex with methotrexate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Methotrexate recognition by the human reduced folate carrier SLC19A1.

Wright, N.J.Fedor, J.G.Zhang, H.Jeong, P.Suo, Y.Yoo, J.Hong, J.Im, W.Lee, S.Y.

(2022) Nature 609: 1056-1062

  • DOI: https://doi.org/10.1038/s41586-022-05168-0
  • Primary Citation of Related Structures:  
    7TX6, 7TX7, 8DEP

  • PubMed Abstract: 

    Folates are essential nutrients with important roles as cofactors in one-carbon transfer reactions, being heavily utilized in the synthesis of nucleic acids and the metabolism of amino acids during cell division 1,2 . Mammals lack de novo folate synthesis pathways and thus rely on folate uptake from the extracellular milieu 3 . The human reduced folate carrier (hRFC, also known as SLC19A1) is the major importer of folates into the cell 1,3 , as well as chemotherapeutic agents such as methotrexate 4-6 . As an anion exchanger, RFC couples the import of folates and antifolates to anion export across the cell membrane and it is a major determinant in methotrexate (antifolate) sensitivity, as genetic variants and its depletion result in drug resistance 4-8 . Despite its importance, the molecular basis of substrate specificity by hRFC remains unclear. Here we present cryo-electron microscopy structures of hRFC in the apo state and captured in complex with methotrexate. Combined with molecular dynamics simulations and functional experiments, our study uncovers key determinants of hRFC transport selectivity among folates and antifolate drugs while shedding light on important features of anion recognition by hRFC.


  • Organizational Affiliation

    Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reduced folate transporter,Soluble cytochrome b562678Homo sapiensEscherichia coliMutation(s): 2 
Gene Names: SLC19A1FLOT1RFC1cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P41440 (Homo sapiens)
Explore P41440 
Go to UniProtKB:  P41440
PHAROS:  P41440
GTEx:  ENSG00000173638 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P41440
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3
MODEL REFINEMENTPHENIX1.13-2998

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM137421
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM129547
American Heart AssociationUnited States20PRE35210058

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 2.0: 2022-10-05
    Changes: Advisory, Database references, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2022-10-12
    Changes: Database references
  • Version 2.2: 2024-03-13
    Changes: Data collection, Source and taxonomy