Structure of the human marker of self 5-transmembrane receptor CD47

CD47 is the only 5-transmembrane (5-TM) spanning receptor of the immune system. Its extracellular domain (ECD) is a cell surface marker of self that binds SIRPα and inhibits macrophage phagocytosis, and cancer immuno-therapy approaches in clinical trials are focused on blocking CD47/SIRPα interaction. We present the crystal structure of full length CD47 bound to the function-blocking antibody B6H12. CD47 ECD is tethered to the TM domain via a six-residue peptide linker (114RVVSWF119) that forms an extended loop (SWF loop), with the fundamental role of inserting the side chains of W118 and F119 into the core of CD47 extracellular loop region (ECLR).


Fig: Overall structure of CD47BRIL-B6H12 complex, ECLR, and TMD: a CD47BRIL-B6H12 complex structure showing the Fab (light and heavy chains shown as pink and gray cartoon respectively), the ECD (green cartoon), and the TMD helices (helix I, blue; helix II, light green; helix III, orange; helix IV, gray and helix V light orange). The CD47 ECLR is formed by the ECL1 (orange tube), ECL2 (gray tube), and the 117SWF119 loop (green surface shown for W118 and F119). The N-linked glycans are shown as sticks with yellow carbons. The gray lines represent the approximate extracellular and intracellular membrane boundaries. b Close up view of the receptor ECLR showing all the three ECLR loops and important residues (side chains shown as sticks and transparent surfaces). The location of the helical kink in helix I centered on P131 (side chain shown as sticks) is also shown. c Top view of CD47 TMD bundle from the extracellular side showing the position of helices and orientation of the three extracellular loops with respect to the helices. d View of the TM bundle from the intracellular side. The side chain of residues in the IC hydrogen bond network are shown as sticks and labeled.

Using hydrogen-deuterium exchange and molecular dynamics simulations we show that CD47’s ECLR architecture, comprised of two extracellular loops and the SWF loop, creates a molecular environment stabilizing the ECD for presentation on the cell surface. These findings provide insights into CD47 immune recognition, signaling and therapeutic intervention.

Fenalti, G., Villanueva, N., Griffith, M. et al. Structure of the human marker of self 5-transmembrane receptor CD47. Nat Commun 12,5218 (2021).

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