Transmembrane protein CD69 acts as an S1PR1 agonist

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Abstract

The activation of Sphingosine-1-phosphate receptor 1 (S1PR1) by S1P promotes lymphocyte egress from lymphoid organs, a process critical for immune surveillance and T cell effector activity. Multiple drugs that inhibit S1PR1 function are in use clinically for the treatment of autoimmune diseases. Cluster of Differentiation 69 (CD69) is an endogenous negative regulator of lymphocyte egress that interacts with S1PR1 in cis to facilitate internalization and degradation of the receptor. The mechanism by which CD69 causes S1PR1 internalization has been unclear. Moreover, although there are numerous class A GPCR structures determined with different small molecule agonists bound, it remains unknown whether a transmembrane protein per se can act as a class A GPCR agonist. Here, we present the cryo-EM structure of CD69-bound S1PR1 coupled to the heterotrimeric G_i complex. The transmembrane helix (TM) of one protomer of CD69 homodimer contacts the S1PR1-TM4. This interaction allosterically induces the movement of S1PR1-TMs 5-6, directly activating the receptor to engage the heterotrimeric G_i. Mutations in key residues at the interface affect the interactions between CD69 and S1PR1, as well as reduce the receptor internalization. Thus, our structural findings along with functional analyses demonstrate that CD69 acts in cis as a protein agonist of S1PR1, thereby promoting G_i-dependent S1PR1 internalization, loss of S1P gradient sensing, and inhibition of lymphocyte egress.

Data availability

The 3D cryo-EM density maps have been deposited in the Electron Microscopy Data Bank under the accession number EMD-29861. Atomic coordinates for the atomic model have been deposited in the Protein Data Bank under the accession number 8G94. All other data needed to evaluate the conclusions in the paper are present in the paper and/or the supplementary materials.

The following data sets were generated

1. Li X
2. et al
(2023) Transmembrane protein CD69 acts as an S1PR1 agonist
PDB, 8G94.

https://www.rcsb.org/structure/8G94
1. Li X
2. et al
(2023) Transmembrane protein CD69 acts as an S1PR1 agonist
EMBD, EMD-29861.

https://www.ebi.ac.uk/emdb/EMD-29861

Article and author information

Author details

Hongwen Chen

Department of Molecular Genetics, The University of Texas Southwestern Medical Center, Dallas, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1065-9808
Yu Qin

Department of Molecular Genetics, The University of Texas Southwestern Medical Center, Dallas, United States

Competing interests
The authors declare that no competing interests exist.
Marissa Chou

Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, United States

Competing interests
The authors declare that no competing interests exist.
Jason G Cyster

Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States

For correspondence
jason.cyster@ucsf.edu

Competing interests
The authors declare that no competing interests exist.
Xiaochun Li

Department of Molecular Genetics, The University of Texas Southwestern Medical Center, Dallas, United States

For correspondence
xiaochun.li@utsouthwestern.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-0177-0803

Funding

National Institutes of Health (P01 HL160487)

Xiaochun Li

National Institutes of Health (R01 GM135343)

Xiaochun Li

Welch Foundation (I-1957)

Xiaochun Li

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.