9JRN | pdb_00009jrn

outward-open hSLC19A1 + TPP

• PDB DOI: https://doi.org/10.2210/pdb9JRN/pdb
• EM Map EMD-61761: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2024-09-29 Released: 2025-02-26 
• Deposition Author(s): Zhang, Q.X., Liu, K.X., Gao, P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular basis of SLC19A1-mediated folate and cyclic dinucleotide transport.

Zhang, Q., Zhang, X., Liu, K., Zhu, Y., Nie, X., Ma, J., Sun, P., Li, Z., Gao, Y., Liu, S., Gao, A., Zhang, L., Gao, P.

(2025) Nat Commun 16: 3146-3146

• PubMed: 40175380 
• DOI: https://doi.org/10.1038/s41467-025-58378-1
• Primary Citation Related Structures: 
  9JOZ, 9JRI, 9JRK, 9JRL, 9JRM, 9JRN


• PubMed Abstract: 
  

  The solute carrier protein SLC19A1 is crucial for transporting folate nutrients, antifolate chemotherapeutics, and more recently cyclic dinucleotides (CDNs) immune transmitters, influencing various physiological and pathological processes. While the inward-open state of human SLC19A1 (hSLC19A1) has been previously described, key aspects regarding its conformational dynamics, substrate selectivity, and precise mechanisms underlying CDNs transport remain elusive. Using an antibody-facilitated conformation screening strategy, we present cryo-electron microscopy structures of hSLC19A1 in its outward-open state with and without bound substrates, revealing detailed mechanisms of substrate recognition and conformational changes during transport. We identify both general and specific features for folate/antifolate recognition, including an SLC19A1-specific pocket for accommodating γ-carboxylate-modified antifolates. Intriguingly, CDNs bind as monomers within the canonical pocket of outward-open hSLC19A1, contrasting with dimeric binding in inward-open structures. Together with functional assays, these findings provide a framework for developing antifolate drugs and CDN-targeted therapies, advancing our understanding of SLC19A1's physiological and therapeutic functions.

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Organizational Affiliation: 
• Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, China.
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, China. [e-mail].
Science and Technology Innovation Center, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, China. [e-mail].
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
Science and Technology Innovation Center, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 77.91 kDa 
• Atom Count: 3,129 
• Modeled Residue Count: 386 
• Deposited Residue Count: 690 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,Reduced folate transporter,fusion protein	A	690	Escherichia coli, Homo sapiens	Mutation(s): 0  Gene Names: cybC, SLC19A1, FLOT1, RFC1 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP (Subject of Investigation/LOI)	B [auth A]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Zhang, Q.X., Liu, K.X., Gao, P.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release
  
• Version 1.1: 2025-04-23
  Changes: Data collection, Database references
• Version 1.2: 2025-07-23
  Changes: Data collection