7XQ1

Structure of hSLC19A1+2'3'-CDAS


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Recognition of cyclic dinucleotides and folates by human SLC19A1.

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

(2022) Nature 612: 170-176

  • DOI: https://doi.org/10.1038/s41586-022-05452-z
  • Primary Citation of Related Structures:  
    7XPZ, 7XQ0, 7XQ1, 7XQ2, 8GOE, 8GOF

  • PubMed Abstract: 

    Cyclic dinucleotides (CDNs) are ubiquitous signalling molecules in all domains of life 1,2 . Mammalian cells produce one CDN, 2'3'-cGAMP, through cyclic GMP-AMP synthase after detecting cytosolic DNA signals 3-7 . 2'3'-cGAMP, as well as bacterial and synthetic CDN analogues, can act as second messengers to activate stimulator of interferon genes (STING) and elicit broad downstream responses 8-21 . Extracellular CDNs must traverse the cell membrane to activate STING, a process that is dependent on the solute carrier SLC19A1 22,23 . Moreover, SLC19A1 represents the major transporter for folate nutrients and antifolate therapeutics 24,25 , thereby placing SLC19A1 as a key factor in multiple physiological and pathological processes. How SLC19A1 recognizes and transports CDNs, folate and antifolate is unclear. Here we report cryo-electron microscopy structures of human SLC19A1 (hSLC19A1) in a substrate-free state and in complexes with multiple CDNs from different sources, a predominant natural folate and a new-generation antifolate drug. The structural and mutagenesis results demonstrate that hSLC19A1 uses unique yet divergent mechanisms to recognize CDN- and folate-type substrates. Two CDN molecules bind within the hSLC19A1 cavity as a compact dual-molecule unit, whereas folate and antifolate bind as a monomer and occupy a distinct pocket of the cavity. Moreover, the structures enable accurate mapping and potential mechanistic interpretation of hSLC19A1 with loss-of-activity and disease-related mutations. Our research provides a framework for understanding the mechanism of SLC19-family transporters and is a foundation for the development of potential therapeutics.


  • Organizational Affiliation

    CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reduced folate transporter544Homo sapiensMutation(s): 0 
Gene Names: SLC19A1FLOT1RFC1
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
Expand
  • 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],
C [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: 3.40 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)China32130057
National Natural Science Foundation of China (NSFC)China31922037
National Natural Science Foundation of China (NSFC)China81921005
National Natural Science Foundation of China (NSFC)China32171219
National Natural Science Foundation of China (NSFC)China82001681

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2022-12-14
    Changes: Database references
  • Version 1.3: 2024-07-03
    Changes: Data collection