Crista junctions (CJs) are tubular invaginations of the inner membrane of 
mitochondria that connect the inner boundary with the cristae membrane. These 
architectural elements are critical for mitochondrial function. The yeast inner 
membrane protein Fcj1, called mitofilin in mammals, was reported to be 
preferentially located at CJs and crucial for their formation. Here we 
investigate the functional roles of individual domains of Fcj1. The most 
conserved part of Fcj1, the C-terminal domain, is essential for Fcj1 function. 
In its absence, formation of CJ is strongly impaired and irregular, and stacked 
cristae are present. This domain interacts with full-length Fcj1, suggesting a 
role in oligomer formation. It also interacts with Tob55 of the translocase of 
outer membrane β-barrel proteins (TOB)/sorting and assembly machinery (SAM) 
complex, which is required for the insertion of β-barrel proteins into the outer 
membrane. The association of the TOB/SAM complex with contact sites depends on 
the presence of Fcj1. The biogenesis of β-barrel proteins is not significantly 
affected in the absence of Fcj1. However, down-regulation of the TOB/SAM complex 
leads to altered cristae morphology and a moderate reduction in the number of 
CJs. We propose that the C-terminal domain of Fcj1 is critical for the 
interaction of Fcj1 with the TOB/SAM complex and thereby for stabilizing CJs in 
close proximity to the outer membrane. These results assign novel functions to 
both the C-terminal domain of Fcj1 and the TOB/SAM complex.