murine SMPDL3A bound to sulfate

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

Starting Model: experimental
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SMPDL3A is a cGAMP-degrading enzyme induced by LXR-mediated lipid metabolism to restrict cGAS-STING DNA sensing.

Hou, Y.Wang, Z.Liu, P.Wei, X.Zhang, Z.Fan, S.Zhang, L.Han, F.Song, Y.Chu, L.Zhang, C.

(2023) Immunity 56: 2492-2507.e10

  • DOI: https://doi.org/10.1016/j.immuni.2023.10.001
  • Primary Citation of Related Structures:  
    8W6P, 8W6R

  • PubMed Abstract: 

    Lipid metabolism has been associated with the cyclic guanosine monophosphate (GMP)-AMP synthase (cGAS) stimulator of interferon genes (STING) DNA-sensing pathway, but our understanding of how these signals are integrated into a cohesive immunometabolic program is lacking. Here, we have identified liver X receptor (LXR) agonists as potent inhibitors of STING signaling. We show that stimulation of lipid metabolism by LXR agonists specifically suppressed cyclic GMP-AMP (cGAMP)-STING signaling. Moreover, we developed cyclic dinucleotide-conjugated beads to biochemically isolate host effectors for cGAMP inhibition, and we found that LXR ligands stimulated the expression of sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A), which is a 2'3'-cGAMP-degrading enzyme. Results of crystal structures suggest that cGAMP analog induces dimerization of SMPDL3A, and the dimerization is critical for cGAMP degradation. Additionally, we have provided evidence that SMPDL3A cleaves cGAMP to restrict STING signaling in cell culture and mouse models. Our results reveal SMPDL3A as a cGAMP-specific nuclease and demonstrate a mechanism for how LXR-associated lipid metabolism modulates STING-mediated innate immunity.

  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acid sphingomyelinase-like phosphodiesterase 3a422Mus musculusMutation(s): 0 
Gene Names: Smpdl3aAsml3a
EC: 3.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for P70158 (Mus musculus)
Explore P70158 
Go to UniProtKB:  P70158
IMPC:  MGI:1931437
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70158
Glycosylation Sites: 4Go to GlyGen: P70158-1
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.374α = 90
b = 86.374β = 90
c = 79.886γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32070875
National Natural Science Foundation of China (NSFC)China82241074

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release