Structure of the Fanconi Anemia Core–UBE2T complex poised to ubiquitinate bound FANCI–FANCD2

The Fanconi Anemia (FA) pathway is essential for the repair of DNA interstrand crosslinks (ICLs). The pathway is activated when a replication fork stalls because of an ICL or other replication stress. A central event in pathway activation is the mono-ubiquitination of the FANCI-FANCD2 (ID) complex by the FA Core complex, a ubiquitin ligase of nine subunits. Here we describe the cryo-EM structures of the 1.1 MDa FA Core at 3.1 angstroms, except for the FANCA subunit at 3.4, and of the complex containing Core, ID and the UBE2T ubiquitin conjugating enzyme at 4.2 angstroms. The Core has unusual stoichiometry with two copies of FANCB, FAAP100, FANCA, FAAP20, FANCG, FANCL, but only a single copy of FANCC, FANCE and FANCF. This is due to homodimers of FANCA and FANCB having incompatible 2-fold symmetry, resulting in an overall asymmetric assembly of the other subunits. The asymmetry is crucial, as it prevents the binding of a second FANC-C-E-F sub-complex that inhibits UBE2T recruitment by FANCL, and instead creates an ID binding site. The single active FANCL-UBE2T binds next to the FANCD2 ubiquitination site, prying open the FANCI-FANCD2 interface within which the ubiquitination sites are buried. These structures and biochemical data indicate a single active site ubiquitinates FANCD2 and FANCI sequentially, shedding light on a central event in the FA pathway.