(R3785) Cryo-EM Structure of Atypical Chemokine Receptor 3 (ACKR3) in Complex with its Endogenous Ligand CXCL12

Yu-Chen Yen (Purdue University)| Christopher Schafer (University of California, San Diego)| Martin Gustavsson (University of Copenhagen)| Pawel Dominik (Pfizer Pharmaceutical Company)| Martin Kossiakoff (University of Chicago)| Tracy Handel (University of California, San Diego)| John Tesmer (Purdue University)

CXCR7 is a seven-transmembrane chemokine receptor that is involved in different stages of cancer progression. Unlike canonical G-protein coupled receptors (GPCRs), CXCR7 has not been reported to activate signaling pathways through heterotrimeric G-proteins when it binds to its endogenous ligand, CXCL12. Thus, one of the proposed molecular mechanisms for CXCR7 in cancer progression is through arrestin-mediated signaling and/or by active sequestration of chemokine ligands. We determined by cryo-electron microscopy (cryo-EM) the 3.3 Å structure of CXCR7 in complex with a higher affinity variant of CXCL12 as well as extracellularly and intracellularly directed Fabs (CID25 and CID24, respectively) used as fiducials to aid the determination. CXCL12 binds to ACKR3 in a unique way from other chemokine complexes reported to date. CID25 stabilizes the extracellular loop 2 (ECL2) of the receptor and the 30s loop of chemokine, whereas the complementarity determining region 3 (CDR3) of CID24 inserts into the cytoplasmic pocket of the receptor, which overall adopts a conformation consistent with those of other GPCRs in an active configuration. The biochemical data demonstrates that CID25 does not affect β-arrestin recruitment, indicating that the conformation of CID25-bound receptor is physiologically relevant. The CXCR7-CXCL12 structure reveals the interactions formed by the N-terminus of CXCL12 in the orthosteric binding pocket of CXCR7 and how the N-terminus of the receptor contributes to the core β-sheet of CXCL12. The structure model may also guide the drug discovery targeting CXCR7 in the future and help explain its perceived bias towards GRK/arrestin signaling.

Support or Funding Information

NIH 1R01CA254402 NIH 1R01GM117424