Necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are secreted by several phytopathogenic bacteria, fungi and oomycetes. They trigger leaf necrosis and immunity-associated responses in various dicotyledonous plants. Our recent studies showed that glycosylinositol phosphorylceramides (GIPC), a major class of plant sphingolipids in plant cell plasma membranes, are target molecules for NLP proteins. Structural studies using X-ray crystallography complemented with other biochemical and biophysical experiments revealed that a NLP protein from the phytopathogenic oomycete Pythium aphanidermatum (NLPPya) forms complexes with terminal hexose moieties of these sphingolipids. NLPPya binding to GIPC head groups induces several conformational changes, such as widening of the L2-L3-lined crevice and a 2.9Å movement of magnesium ion towards the center of the protein relative to its position in ligand-free NLPPya, which is followed by membrane attachment and host cell lysis. Structure based point mutations of residues in NLPPya protein predicted to be crucial for membrane anchoring resulted in plant toxin resistance. These results propose a model of early steps of NLPPya membrane interaction as well as suggest an explanation for selectivity of NLP proteins for dicotyledonous plants due to steric limitations of GIPC glycoside modules binding into a ligand binding cleft of NLPPya.