Fibroblast growth factors (FGFs) constitute a large family of heparin-binding growth factors with diverse biological activities. FGF9 was originally described as glia-activating factor and is expressed in the nervous system as a potent mitogen for glia cells. Unlike most FGFs, FGF9 forms dimers in solution with a K d of 680 nM. To elucidate the molecular mechanism of FGF9 dimerization, the crystal structure of FGF9 was determined at 2.2 Å resolution. FGF9 adopts a -trefoil fold similar to other FGFs. However, unlike other FGFs, the N-and C-terminal regions outside the -trefoil core in FGF9 are ordered and involved in the formation of a 2-fold crystallographic dimer. A significant surface area (>2000 Å 2 ) is buried in the dimer interface that occludes a major receptor binding site of FGF9. Thus, we propose an autoinhibitory mechanism for FGF9 that is dependent on sequences outside of the -trefoil core. Moreover, a model is presented providing a molecular basis for the preferential affinity of FGF9 toward FGFR3.The mammalian fibroblast growth factor (FGF) 1 family contains at least 22 distinct polypeptides (FGF1-FGF22) that are expressed in a specific spatial and temporal pattern (1-5). FGFs play important roles in numerous physiological and pathological processes (1-5). Members of the FGF family share between 10 and 55% sequence identity (6). Crystal structures of FGF1 (7), FGF2 (7-9), and FGF7 (10), have revealed a common core FGF structure consisting of three copies of a four-stranded -sheet, known as a -trefoil fold. All FGFs contain N-and C-terminal segments outside the -trefoil core. However, the length of these segments, especially the C termini, varies greatly among different FGFs. In FGF1, FGF2, FGF4, and FGF7, the end of polypeptide chain virtually coincides with the end of the -trefoil fold. Consequently, these FGFs have extremely short C-terminal segments. In contrast, other FGFs, such as FGF3, FGF5, and FGF8, have long C-terminal extensions. The functional relevance of these N-and C-terminal extensions remains uncharacterized. FGF9 (glia-activating factor) was purified as a heparin-binding, secreted glycoprotein from cultured human glioma cell line NMC-G1 (11). FGF9 shows 30% sequence identity with the prototypical FGF family members, FGF1 and FGF2 (12). Purified FGF9 is mitogenic for many types of cultured cells including glia cells, oligodendrocyte type 2 astrocyte progenitor cells, smooth muscle cells, pheochromocytoma PC12 cells, and BALB/3T3 fibroblasts (11). Because FGF9, unlike FGF1 and FGF2, has no effect on human umbilical vein endothelial cells, it is suggested that FGF9 may have a unique receptor specificity (11). In fact, biochemical studies performed utilizing various soluble FGFR-alkaline phosphatase fusion proteins and genetically engineered cells expressing different full-length FGFRs have demonstrated that FGF9 binds preferentially to the IIIc form of FGFR3 (13-15).FGF9, like prototypical FGFs, does not have a typical secretory signal peptide. Yet, it is still glycosylated and...