9JRM | pdb_00009jrm

outward-open hSLC19A1 + 2'3'-CDAS


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41467-025-58378-1
  • Primary Citation of 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.


  • Organizational Affiliation
    • Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Reduced folate transporter,Soluble cytochrome b562,Reduced folate transporter,fusion protein690Escherichia coliHomo sapiensMutation(s): 0 
Gene Names: cybCSLC19A1FLOT1RFC1
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41440
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GJF (Subject of Investigation/LOI)
Query on GJF

Download Ideal Coordinates CCD File 
B [auth A](1~{R},3~{S},6~{R},8~{R},9~{R},10~{S},12~{S},15~{R},17~{R},18~{R})-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanylidene)-3,12-bis(sulfanyl)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecane-9,18-diol
C20 H24 N10 O10 P2 S2
IZJJFUQKKZFVLH-ZPTFDBAZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

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