The 95 kDa subunit a of eukaryotic V-ATPases consists of a C-terminal, ion-translocating part and an N-terminal cytosolic domain. The latter’s N-terminal domain (~40 kDa) is described to bind in an acidification-dependent manner with cytohesin-2 (ARNO), giving the V-ATPase the putative function as pH-sensing receptor. Recently, the solution structure of the very N-terminal segment of the cytosolic N-terminal domain has been solved. Here we produced the N-terminal truncated form SCa104-363 of the N-terminal domain (SCa1-363) of the Saccharomyces cerevisiae V-ATPase and determined its low resolution solution structure, derived from SAXS data. SCa104-363 shows an extended S-like conformation with a width of about 3.88 nm and a length of 11.4 nm. The structure has been superimposed into the 3D reconstruction of the related A1AO ATP synthase from Pyrococcus furiosus, revealing that the SCa104-363 fits well into the density of the collar structure of the enzyme complex. To understand the importance of the C-terminus of the protein SCa1-363, and to determine the localization of the N- and C-termini in SCa104-363, the C-terminal truncated form SCa106-324 was produced and analyzed by SAXS. Comparison of the SCa104-363 and SCa106-324 shapes showed that the additional loop region in SCa104-363 consists of the C-terminal residues. Whereas SCa104-363 is monomeric in solution, SCa106-324 forms a dimer, indicating the importance of the very C-terminus in structure formation. Finally, the solution structure of SCa104-363 and SCa106-324 will be discussed in terms of the topological arrangement of subunit a and cytoheisn-2 in V-ATPases.