9XHI

Structure of the CCL21-CCR7-Gi-scFv16 complex

Summary for 9XHI

• Entry DOI: 10.2210/pdb9xhi/pdb
• EMDB information: 66875
• Descriptor: C-C motif chemokine 21, C-C chemokine receptor type 7,Non structural polyprotein, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2,Guanine nucleotide-binding protein G(i) subunit alpha-1, ... (6 entities in total)
• Functional Keywords: chemokine, chemokine receptor, gpcr, membrane protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 6
• Total formula weight: 240285.29

Authors

Tsutsumi, N.,Nishikawa, K.,Fujiyoshi, Y. (deposition date: 2025-11-01, release date: 2026-04-22, Last modification date: 2026-05-06)

Primary citation

Tanaka, K.,Nishikawa, K.,Shiimura, Y.,Fujiyoshi, Y.,Tsutsumi, N.
Structural insights into biased signaling at chemokine receptor CCR7.
Proc.Natl.Acad.Sci.USA, 123:e2533975123-e2533975123, 2026

PubMed Abstract: CC chemokine receptor 7 (CCR7), which orchestrates adaptive immunity, exhibits a phenomenon known as biased agonism. CCL19 induces robust G-protein signaling and β-arrestin recruitment, leading to transient signaling. In contrast, CCL21 preferentially activates G-protein pathways with minimal arrestin engagement, resulting in sustained signaling and differential functional outcomes. Here, we present the cryo-EM structures of the human CCR7-G complex with either CCL19 or CCL21. The structures reveal that while both engage a conserved orthosteric pocket, they adopt markedly distinct binding poses. Notably, the compact 30s loop of CCL21 inserts deeply into the receptor's extracellular vestibule, whereas the corresponding loop of CCL19 rests atop extracellular loop 2. Molecular dynamics simulations further reveal that these distinct binding modes induce differential intracellular dynamics, linked to the rotameric state of Y83 at the intracellular end of transmembrane helix 1. We demonstrate that CCL19 stabilizes a flexible conformational ensemble with a highly dynamic helix 8, creating a lateral opening favorable for GPCR kinase engagement. Conversely, CCL21 restricts this flexibility, locking the receptor in a state that precludes kinase interaction while maintaining G-protein coupling. Corroborated by functional data, these findings provide key insights into the structural basis of biased agonism at CCR7 and establish a foundation for rational design of pathway-selective immunomodulators.

PubMed: 42054364
DOI: 10.1073/pnas.2533975123

Experimental method

ELECTRON MICROSCOPY (3.2 Å)