Human APOBEC3G (A3G) is an innate immunity protein against human immunodeficient virus (HIV) by deaminating cytosine into uracil on reverse transcripted single-stranded DNA of HIV. Vif, a HIV protein that functions as a substrate receptor together with Elongin BC complex and CBF\beta, for the Cullin 5-based E3 ligase complex, leads to ubiquitination and subsequent proteosomal degradation of A3G. To date, the structural information of this A3G-Vif bound E3 ligase complex is limited, as the structure of full-length A3G is not revealed since its self-oligomerizing nature of A3G. Here, we report three dimensional reconsturction of the hexameric complex of full-length A3G and Vif–CBF\beta–Elongin B–Elongin C–Cullin5 by using negative staining electron microscopy and chemical crosslinking. YFP tagged on N-terminal domain of A3G revealed that A3G dimerizes through its N-terminal domain, also A3G and Vif–CBF\beta– ElonginB–ElonginC–Cullin5 is forming 2:1 complex. Chemical crosslinking of lysines, followed by mass spectrometry also provides an evidence of N-terminal dimerization of A3G, while having a novel hydrophobic interface consisted of helix α6 to helix α6’. Full-model construction of E3 ligase, A3G–Vif–CBF\beta–Elongin B–Elongin C–Cul5–Rbx1–UbcH5–ubiquitin, providing structural basis of Vif-mediated A3G ubiquitination mechanism.