Correction for Yu et al., Structural insights into sphingosine-1-phosphate receptor activation

Biochemistry Correction for “Structural insights into sphingosine-1-phosphate receptor activation,” by Leiye Yu, Licong He, Bing Gan, Rujuan Ti, Qingjie Xiao, Hongli Hu, Lizhe Zhu, Sheng Wang, and Ruobing Ren, which published April 11, 2022; 10.1073/pnas.2117716119 (Proc. Natl. Acad. Sci. U.S.A. 119, e2117716119).

The authors note that Xin Yang should be added to the author list between Qingjie Xiao and Hongli Hu. Xin Yang should be credited with contributing new reagents and analyzing data. The corrected author line, affiliation line, and author contributions appear below. The online version has been corrected.

The authors note that on page 5, left column, first full paragraph, line 13, “CBP-307 in the deep mode is inserted 1.8 Å deeper into the pocket” should instead appear as “CBP-307 in the deep mode is inserted 1.5 Å deeper into the pocket.” On page 6, left column, first paragraph, line 2, “the amino group forms a hydrogen bond with S105” should instead appear as “the nitrogen atom of azetidine forms a weak hydrogen bond with S105.” Also on page 6, right column, first paragraph, line 1, “the deeper insertion of CBP-307 makes its amino group closer to E121^3.29” should instead appear as “the deeper insertion of CBP-307 makes its nitrogen atom of azetidine closer to E121^3.29.” On page 7, left column, first paragraph, line 4, “the CBP-307 in the shallow mode inserted deeper after about 50 ns and stayed in a similar position to the deep mode for longer than 1,100 ns” should instead appear as “the CBP-307 in the shallow mode inserted deeper after about 20ns and stayed in a similar position to the deep mode for longer than 250ns.” The online version has been corrected.

The authors note that Figs. 1, 4, and 5 appeared incorrectly. The legend for Fig. 4 also appeared incorrectly. The corrected figures and their legends, including a corrected legend for Fig. 4, appear below. The online version has been corrected.

Fig. 1.

Cryo-EM maps and structures of human S1PR1 with G_i and agonist d18:1 S1P, (S)-FTY720-P, or CBP-307. (A) Structural formulas of three agonists: d18:1 S1P, (S)-FTY720-P, and CBP-307. (B) Cryo-EM maps of human S1PR1 with Gi and agonist d18:1 S1P, (S)-FTY720-P, or CBP-307. The densities of S1PR1, G_αi, G_β, G_γ, and scFv16 are shown in marine, pale green, pink, wheat, and gray, respectively. (C) Structural models of human S1PR1 with G_i, scFv16, and agonist d18:1 S1P (PDB ID code 7VIE), (S)-FTY720-P (PDB ID code 7VIF), or CBP-307 (PDB ID code 7VIG). S1PR1, G_αi, G_β, G_γ, and scFv16 are shown in marine, pale green, light blue, wheat, and gray, respectively. Ligands in density (yellow) are shown on the right side of the models. (D) The extracellular lid of S1PR1 is shown in the top and side views (surface and cartoon modes). N-helix, ECL1/2, and TM helices are pink, orange, and marine, respectively.

Fig. 4.

CBP-307 binding with S1PR1 in two binding modes. (A) A cutaway representation of two binding modes of CBP-307 bound S1PR1 at the level of binding pocket and colored according to surface electrostatic potential with cut surface shown in gray. CBP-307 in shallow mode is colored in wheat. CBP-307 in deep mode is colored in cyan. CBP-307 is shown in sticks. (B) Superposition of two binding modes of CBP-307. CBP-307 in deep mode inserts into the pocket deeper with a 1.5-Å distance than shallow mode. CBP-307 is shown and colored as in A. (C) CBP-307 is modeled in two density maps. (D) The effects of Y29A, K34A, N101^2.60A, R120^3.28A, and E121^3.29A mutations of S1PR1 on CBP-307 induced Gi signal activation measured by Gi dissociation assay (BERT assay). All data are mean ± SEM of three independent experiments for wild-type or mutants. (E) The key residues interacted with the polar groups of CBP-307 in shallow mode. S1PR1 and CBP-307 are shown in gray and yellow, respectively. CBP307, Y29, K34, N101^2.60, S105, G106, T109, R120^3.28A, and E121^3.29 are shown in sticks. Dashed lines indicate the polar interactions between CBP-307 and K34, N101^2.60, and S105 with distances. (F) The key residues interacted with the polar groups of CBP-307 in deep mode. S1PR1 and CBP-307 are shown in marine and cyan, respectively. CBP307, Y29, K34, N101^2.60, S105, G106, T109, R120^3.28A, and E121^3.29 are shown in sticks. Dashed lines with distances indicate the polar interactions between CBP-307 and Y29, N101^2.60, G106, and T109.

Fig. 5.

Activation of S1PR1 by CBP-307. (A) A cutaway representation of d18:1 S1P in the S1PR1–G_i–d18:1 S1P model and superimposed two CBP-307 binding modes with d18:1 S1P in the S1PR1–G_i–d18:1 S1P model. The cutaway surface of S1PR1 with d18:1 S1P is shown at the level of binding pocket and colored according to surface electrostatic potential with cut surface shown in gray. d18:1 S1P and CBP-307 are shown in sticks. d18:1 S1P, CBP-307 (shallow), and CBP-307 (deep) are shown in violet, wheat, and cyan, respectively. (B) Superposition of ML056 with CBP-307–inactive and two CBP-307–bound active forms. ML056, CBP-307–shallow, and CBP-307–deep are shown in sticks colored in green, yellow, and cyan, respectively. Residues near the isobutyl group, including L128^3.36, F210^5.47, and F273^6.52 in S1PR1–ML056, S1PR1–CBP-307 (shallow), and S1PR1–CBP-307 (deep), are shown in sticks and colored in green, gray, and marine, respectively. (C) The polar interactions of Gi and S1PR1 with CBP-307 in two modes are similar. S1PR1–CBP-307 (shallow) and S1PR1–CBP-307 (deep) are shown in gray and marine, respectively. The helix 5 of G_αi in S1PR1–CBP-307 (shallow) and S1PR1–CBP-307 (deep) are shown in yellow and wheat, respectively. Residues on S1PR1 and helix 5 of G_αi are shown in sticks. (D) The N-terminal helix of G_αi rich in positive charge residues at a closer position to the membrane in the CBP-307 deep-mode structure. CBP-307 deep and shallow modes are colored in marine and gray, respectively. The positive charge residues (K10, K17, R21, R24, and R32) on the N-terminal helix of G_αi are shown in sticks in D, Inset.

The authors note that the structural parameters in Supporting Table S1 in the SI Appendix appeared incorrectly. Additionally, the CBP-307 structures in Figs. S8, S9, S10, and S12 appeared incorrectly. The SI Appendix has been corrected online.