The ephrin family of membrane proteins binds Eph tyrosine kinase receptors. We have previously shown that ephrin-B3 also binds to heparan sulfate proteoglycans (HSPGs). We now show that ephrin-B3 can bind both secretory and cell associated PGs, such as agrin, collagen XVIII, Perlecan, and CD44, and indicate that such interaction with cell associated PGs involves a complex including 20 and 45 kDa proteins. Ephrin-B3 binding to HEK-293T cells is blocked by a secretory variant of CD44 (v3-v10), while over-expression of membrane associated CD44 increased ephrin-B3 binding. In addition, ephrin-B3 precipitated CD44 expressed by the oral squamous carcinoma cell line H376. Moreover, ephrin-B3 binding affinities to heparin and CD44 in solution was strong. In conclusion, we have identified secretory and cell associated PGs with high ability to bind ephrin-B3 and suggest that ephrin-B3 can bind to a protein complex organized by a membrane associated PG. (C) 2018 Elsevier Inc. All rights reserved.