The RUN domain, named after RPIP8, unc-14 and NESCA, is organized into six conserved blocks (A-F), which are predicted to constitute the 'core' of a globular structure tolerating insertions of considerable length between the conserved blocks. The RUN domain is found in one or two copies in several proteins that are linked particularly to the functions of GTPases in the Rap and Rab families. RUN domains can be associated with TBC/rab GAP (see <PDOC50086>), FYVE (see <PDOC50178>), DENN, SH3 (see <PDOC50002>), DAG/PE-binding (see <PDOC00379>), PLAT/LH2, PH (see <PDOC50003>) or PX (see <PDOC50195>) domains. The RUN domain may have a role in the interaction of various proteins with cytoskeletal filaments [2].

The predicted secondary structures of the RUN domain core indicate a predominantly α fold [1].

Some proteins known to contain a RUN domain are listed below:

• Mammalian Rap2 interacting protein 8 (RPIP8). A probable specific effector of the small GTP-binding protein Rap2 in cells exhibiting neuronal properties.
• Human Nesca (new molecule containing SH3 at the C-terminus), an ubiquitously expressed protein.
• Caenorhabditis elegans unc-14, a protein required for axonal elongation and guidance that interacts with the serine/threonine kinase unc-51.
• Mouse GTP-binding protein-associated protein B (GBPAP-B), a protein found in yeast two-hybrid screen with Rab6 and which specifically interacts with this GTPase bound to GTP. It contains two RUN domains.

The profile we developed covers the entire RUN domain.