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Structural basis of CXC chemokine receptor 2 activation and signalling

Abstract

Chemokines and their receptors mediate cell migration, which influences multiple fundamental biological processes and disease conditions such as inflammation and cancer1. Although ample effort has been invested into the structural investigation of the chemokine receptors and receptor–chemokine recognition2,3,4, less is known about endogenous chemokine-induced receptor activation and G-protein coupling. Here we present the cryo-electron microscopy structures of interleukin-8 (IL-8, also known as CXCL8)-activated human CXC chemokine receptor 2 (CXCR2) in complex with Gi protein, along with a crystal structure of CXCR2 bound to a designed allosteric antagonist. Our results reveal a unique shallow mode of binding between CXCL8 and CXCR2, and also show the interactions between CXCR2 and Gi protein. Further structural analysis of the inactive and active states of CXCR2 reveals a distinct activation process and the competitive small-molecule antagonism of chemokine receptors. In addition, our results provide insights into how a G-protein-coupled receptor is activated by an endogenous protein molecule, which will assist in the rational development of therapeutics that target the chemokine system for better pharmacological profiles.

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Data availability

The atomic coordinates for CXCR2–CXCL8 monomer–Gi–scFv16, CXCR2–CXCL8 dimer–Gi–scFv16 and CXCR2–00767013 have been deposited in the Protein Data Bank (PDB) with the accession codes 6LFO, 6LFM and 6LFL, respectively. The electron microscopy maps for CXCR2–CXCL8 monomer–Gi–scFv16 and CXCR2–CXCL8 dimer–Gi–scFv16 have been deposited in the Electron Microscopy Data Bank (EMDB) with the accession codes EMD-0879 and EMD-0877, respectively. All other data are available upon request to the corresponding authors.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China grants 31930060 and 91953202 (Z.-J.L.), CAS Strategic Priority Research Program XDB37030104 (Z.-J.L.), the National Key Research and Development Program of China grant 2018YFA0507000 (T.H.), Shenzhen Institutes of Advanced Technology, CAS grant 1105150101 (S.Y. and S.L.) and the Interdisciplinary Centre for Mathematical and Computational Modelling in Warsaw grants GB70-3 and GB71-3 (S.Y.). We thank the Shanghai Municipal Government and ShanghaiTech University for financial support; J.-L. Liu and N. Chen at the cell expression core, Q.-W. Tan at the cloning core and staff members at the purification and assay cores of the iHuman Institute for their support; and G.-J. Song, I. Wilson and G. Yang for discussions. The cryo-EM data were collected at the Bio-Electron Microscopy Facility, ShanghaiTech University, with the assistance of D.-D. Liu and Y.-H. Liu. The synchrotron radiation experiments were performed at the BL41XU of SPring-8 with approval of the Japan Synchrotron Radiation Research Institute (JASRI) (proposals 2018B2722 and 2019A2522).

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Contributions

K.L. designed the expression constructs, purified the CXCR2–CXCL8–Gi complexes, prepared the final samples for cryo-EM experiments and data collection with the assistance of T.H., prepared the CXCR2–00767013 sample, performed crystallization and participated in the preparation of the figures and manuscript. L.W. performed electron microscopy data processing and structure determination. S.Y. performed the metaMD simulation and edited the manuscript. S.Y. and S.L. performed coarse-grained MD simulation and analysed the results. M.W. and S.Z. performed the molecular docking. Y.X. performed the functional assay. Q.S. assisted with cryo-EM data collection. Z.-J.L. and T.H. conceived the project, supervised the overall studies, analysed the structures and wrote the manuscript.

Corresponding authors

Correspondence to Tian Hua or Zhi-Jie Liu.

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The authors declare no competing interests.

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Peer review information Nature thanks Aashish Manglik and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data figures and tables

Extended Data Fig. 1 CXCR2–CXCL8–Gi–scFv16 sample preparation and cryo-EM data processing.

a, f, Superdex 200 size-exclusion chromatography elution profiles of the purified CXCR2–CXCL8 (dimer)–scFv16 complex (a) and CXCR2–CXCL8 (monomer)–scFv16 complex (f). b, g, SDS–PAGE analysis of the CXCL8 (dimer) complex (b) and CXCL8 (monomer) complex (g) after size exclusion. c, h, Representative cryo-EM image of the CXCR2–CXCL8 (dimer)–scFv16 complex (c) and CXCR2–CXCL8 (monomer)–scFv16 complex (h). Scale bars, 30 nm. d, i, Representative 2D classification showing distinct structural features of each component. Scale bars, 5 nm. e, j, Workflow of cryo-EM data processing for CXCR2–CXCL8 (dimer)–scFv16 complex (e) and CXCR2–CXCL8 (monomer)–scFv16 complex (j). Cryo-EM maps are coloured by local resolution (Å). Gold-standard FSC curves of the CXCR2–CXCL8 (dimer)–scFv16 and CXCR2–CXCL8 (monomer)–Gi–scFv16, indicating the resolution is 3.5 and 3.4 Å at the FSC = 0.143, respectively.

Extended Data Fig. 2 Cryo-EM maps and refined structures.

a, Cryo-EM density map and the model of CXCR2–CXCL8 (dimer)–Gi–scFv16 complex are shown for all transmembrane helices and helix 8 of CXCR2, and the cholesterol molecule. b, Cryo-EM density map and the model of the CXCR2–CXCL8 (monomer)–Gi–scFv16 complex are shown for all transmembrane helices and helix 8 of CXCR2, and the cholesterol molecule. c, d, Cryo-EM maps for the N-terminal residues (3-KELRCQCIK-11) of CXCL8 in the CXCR2–CXCL8 (dimer)–Gi–scFv16 complex (c) and CXCR2–CXCL8 (monomer)–Gi–scFv16 complex (d) structures.

Extended Data Fig. 3 Characterization of the CXCR2–00767013 complex and its comparison with antagonist-bound CCR2, CCR9 and CCR7.

a, Analytical size-exclusion chromatography profile. b, Crystal image. c, The overall structure of the CXCR2-00767013 complex with receptor in blue and PGS in light teal. The antagonist is shown as yellow sticks and sphere. The 2|Fo|–|Fc| map of 00767013 (in the box) is contoured at 1.0σ. d, Crystal packing of CXCR2-00767013. Colour schemes as in c. e, Addition of the allosteric antagonist 00767013 (blue) suppresses β-arrestin 2 recruitment in response to activation by CXCL8 monomer with half-maximum inhibitory concentration (IC50) of 0.62 ± 0.06 nM. The EC50 for monomeric CXCL8 is 0.38 ± 0.00 nM. Data are mean ± s.e.m. (n = 3). fh, Overall structure comparison with CCR2 (PDB code 5T1A) (f), CCR9 (PDB code 5LWE) (g) and CCR7 (PDB code 6QZH) (h). The arrows indicate the relative orientation difference.

Extended Data Fig. 4 Structure comparison of the CXCR2–CXCL8 (dimer)–Gi–scFv16 and CXCR2–CXCL8 (monomer)–Gi–scFv16 complexes.

a, Overall structure comparison of dimeric and monomeric CXCL8-bound CXCR2–Gi–scFv16 complexes. bg, Structure comparison of corresponding components in the two complex structures when superimposed using CXCR2 as reference. CXCL8 (b), CXCR2 (c), Gαi (d), Gβ (e), Gγ (f) and scFv16 (g).

Extended Data Fig. 5 The dynamic process of CXCL8 and CXCR2 recognition.

a, Coarse-grained molecular dynamics simulation of the CXCL8 binding process. CXCL8 was placed 60 Å away from the N terminus of CXCR2. Step 1: after MD simulation, the N terminus of CXCR2 captured CXCL8 via electrostatic interactions. Small contact area was observed at this stage. Step 2: the N terminus of CXCR2 established an initial complex with CXCL8 and the contact area increased (486 ± 6 Å2). However, CXCL8 was still far away from the orthosteric site. Step 3: with the movement of the N terminus of CXCR2, CXCL8 was transferred to the entrance of CXCR2’s orthosteric site (1308 ± 6 Å2). b, The insertion process of CXCL8 sampled by all-atom metaMD simulation. Step 3 (from position a to b: CXCL8 was placed in an initial position that was identical to that step 2 sampled by coarse-grained simulation. After metaMD, CXCL8 was transferred to the vicinity of the CXCR2 orthosteric site. The energy barrier for this step is about 3.6 ± 0.3kcal mol−1. Step 4: by overcoming the energy barrier (6.6 ± 0.3 kcal mol−1) that was formed by ionic interactions between charged residues, the N-terminal tail finally inserts into the CXCR2. c, R.m.s.d. values of molecular dynamics simulations of the N terminus and overall structure of CXCR2–CXCL8 (dimer)–Gi complex during the 1-μs molecular dynamics simulations. See Supplementary Videos 1, 2.

Extended Data Fig. 6 The initial binding process of CXCL8 and CXCR2 in ten independent coarse-gained simulations.

a, The red chart represents the number of residue–residue contacts between CXCL8 with the first 25 residues of the CXCR2 N terminus; the blue chart shows the contacts between CXCL8 with residues beyond first 25 residues in CXCR2. Contact occurs if the residue-residue distance is shorter than 0.47 nm. CXCL8 binds to the 25 residues of the CXCR2 N terminus first in simulations (1–7), CXCL8 binds first to CXCR2 at the position other than N-terminal 25 residues in two simulations (9, 10), and one simulation (8) failed to result contacts. b, c, Representative N-terminal truncation variants’ effects on the agonism of wild-type CXCL8 (CXCL8-WT) and modified monomeric CXCL8 in the β-arrestin 2 recruitment assay. For CXCL8-WT: the EC50 values for CXCR2-WT, CXCR2-NΔ9, CXCR2-NΔ13 and CXCR2-NΔ19 are 0.19 ± 0.00 nM, 0.21 ± 0.00 nM, 0.31 ± 0.00 nM and 0.72 ± 0.04 nM, respectively. For CXCL8-monomer: the EC50 values for CXCR2-WT, CXCR2-NΔ9, CXCR2-NΔ13 and CXCR2-NΔ19 are 0.38 ± 0.00 nM, 0.50 ± 0.00 nM, 0.79 ± 0.12 nM and 1.48 ± 0.02 nM, respectively. Data are mean ± s.e.m. (n = 3).

Extended Data Fig. 7 Comparison of G proteins between CXCR2–CXCL8 (dimer)–Gi and GPCR–Gi, GPCR–Gs and GPCR–G11 complexes.

a, The structure of each GPCR–Gi/Gs/G11 complex is superposed onto CXCR2–CXCL8 (dimer)–Gi using receptor as reference. MOR (PDB code 6DDE), NTS1R (PDB code 6OS9), M1R (PDB code 6OIJ), β2AR (PDB code 3SN6). b, Comparison analysis of the interfaces formed between ICL2 of CXCR2 and Gαi, as well as between ICL2 of β2AR and Gαs. The sequence alignment of residues 34.50 and 34.51 among chemokine receptors is also presented. c, The sequence alignment of key residues which are within 4 Å interaction range in the solved GPCR–G protein complex structures. d, The sequence alignment of key residues involved in the solved chemokine receptors. Orange colour indicates the key residues discovered in the CXCR2–CXCL8–Gi complex.

Extended Data Fig. 8 Activation hallmarks of CXCR2 and the structure comparison of US28–CX3CL1 with the inactive and active CXCR2 structures.

ac, Rearrangements of the PIF motif (a), toggle switch residues (b) and the NPxxY motif (c) between inactive (blue sticks) and active (orange sticks) states of CXCR2. df, Structure comparison of US28–CX3CL1 and inactive CXCR2. Side view (d), extracellular view (e) and intracellular view (f). gi, Structure comparison of US28–CX3CL1 and active CXCR2. Side view (g), extracellular view (h) and intracellular view (i). jl, Structure comparison of toggle switch residues (j), the PIF motif (k) and the NPxxY motif (l) between US28-CX3CL1 and active CXCR2.

Extended Data Fig. 9 Comparison of CXCR1 and CXCR2 and chemokine interactions.

a, Molecular model of the CXCR1–CXCL8 complex. CXCR1 is shown in white cartoon and CXCL8 is shown in red cartoon and shaded surface. b, Hydrophobic interactions between CXCR2 N terminus and CXCL8-A. Red, hydrophilic region; white, hydrophobic region. c, Electrostatic and surface properties of CXCL8 in the CXCL8–CXCR1 complex model. Electrostatic potentials (+8 kT per electron in blue and −8 kT per electron in red) mapped on the surfaces of the CXCL8 calculated at pH 7.0 using the programs PDB2PQR68 and APBS69. d, Diagram of the contacts between the CXCR2 N terminus and the N-loop of CXCL8. Acidic, basic, polar uncharged and hydrophobic residues are coloured red, blue, grey and green, respectively. sY, sulfotyrosine.

Extended Data Table 1 Cryo-EM data collection, model refinement and validation statistics
Extended Data Table 2 Crystal data collection, refinement and validation statistics

Supplementary information

Supplementary Figure 1

The sequence alignment of chemokine receptors using key residues which are within 4 Å interaction range in CXCR2-Gi complex structure as reference.

Reporting Summary

Video 1

: The initial recognition process of CXCL8 and CXCR2 The process was sampled by coarse-grained (CG) long-time scale MD simulations. CXCL8 was placed 60 Å away from the N-terminus of CXCR2. After MD simulation, the N-terminus of CXCR2 captured CXCL8 via electrostatic interactions. N-terminus of CXCR2 established an initial complex with CXCL8. With the movement of the N-terminus of CXCR2, CXCL8 was transferred to the entrance of CXCR2’s orthosteric site.

Video 2

: The N-terminal insertion process of CXCL8 into CXCR2. The process was sampled by all-atom metaMD simulations. CXCL8 was placed in an initial position that was sampled at the last step of CG simulation. After metaMD, CXCL8 was transferred to the vicinity of the CXCR2 orthosteric site. By overcoming the energy barrier that was formed by ionic interactions between charged residues, the N-terminal tail finally inserts into the CXCR2.

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Liu, K., Wu, L., Yuan, S. et al. Structural basis of CXC chemokine receptor 2 activation and signalling. Nature (2020). https://doi.org/10.1038/s41586-020-2492-5

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