Rap2-interacting protein x (RPIPx) is a homolog of RPIP8, a specific effector of Rap2 GTPase. The N-terminal region of RPIP8, which contains the RUN domain, interacts with Rap2. Using cell-free synthesis and NMR, we determined that the region encompassing residues 83-255 of mouse RPIPx, which is 40-residues larger than the predicted RUN domain (residues 113-245), is the minimum fragment that forms a correctly folded protein. This fragment, the RPIPx RUN domain, interacted specifically with Rap2B in vitro in a nucleotide-dependent manner. The crystal structure of the RPIPx RUN domain was determined at 2.0 Å of resolution by the multiwavelength anomalous dispersion (MAD) method. The RPIPx RUN domain comprises eight anti-parallel ␣-helices, which form an extensive hydrophobic core, followed by an extended segment. The residues in the core region are highly conserved, suggesting the conservation of the RUN domain-fold among the RUN domain-containing proteins. The residues forming a positively charged surface are conserved between RPIP8 and its homologs, suggesting that this surface is important for Rap2 binding. In the crystal the putative Rap2 binding site of the RPIPx RUN domain interacts with the extended segment in a segment-swapping manner.The small GTPases of the Ras family function as molecular switches, regulating diverse cellular processes such as proliferation and differentiation (1, 2). They cycle between the GTPbound, activated forms and the GDP-bound, inactivated forms, with the aid of regulatory proteins, such as guanine nucleotide exchange factors, GTPase-activating proteins, and guanine nucleotide dissociation inhibitors. Between the GTP-bound and GDP-bound forms, conformational changes occur in two conserved regions, the switch-I and switch-II regions. The switch-I region encompasses the "effector region," through which the GTP-bound forms interact with their effectors that activate downstream targets.The Ras family consists of Ras (H-, K-, and N-Ras), M-Ras, R-Ras, TC21, Rap1 (Rap1A and B), Rap2 (Rap2A and B), Ral, Rheb, Rin, and Rit (3). Rap1 and Rap2 are very close relatives (ϳ60% sequence identity), and they exhibit ϳ50% sequence identity with Ras (4). Rap1 and Ras share an identical effector region, whereas in Rap2, the single replacement of Ser-39 by Phe is observed. Several experiments have shown that Rap1 functions as an antagonist in Ras-signaling pathways, probably by competing for the Ras effectors (5-8). In contrast, Rap2 did not antagonize Ras-induced transformation (9). Rap2 interacts with Ras effectors, such as Raf, phosphatidylinositol 3-kinase (PI3K), and Ral guanine nucleotide dissociation stimulator (GDS), but it only inhibits the activation of the downstream targets of Raf and PI3K and not RalGDS (10 -12). Furthermore, Rap2 is regulated differently by guanine nucleotide exchange factors and GTPase-activating proteins as compared with Rap1 (10), suggesting that Rap1 and Rap2 have distinct signaling functions.Rap2 interacts with its specific effector, Rap2-interacting protein 8 (RP...