Skorupka Katarzyna A, Matsuoka Kazuhiro, Hassan Bakar, Ghirlando Rodolfo, Balachandran Vanivilasini, Chen Ting-Hua, Walters Kylie J, Schiffer Celia A, Wolf Matthias, Iwatani Yasumasa, Matsuo Hiroshi
Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702, USA.
Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan.
Nat Commun. 2025 Jul 1;16(1):5879. doi: 10.1038/s41467-025-60984-y.
The APOBEC3 family of cytidine deaminases restricts retroviruses like HIV-1 by mutating viral DNA. HIV-1 evades this restriction by producing Vif, which recruits the Cullin-5 (CUL5) E3 ubiquitin ligase complex to promote APOBEC3 degradation. Here we resolve key aspects of this counter-defense mechanism by determining a 3.6 Å cryo-EM structure of chimpanzee APOBEC3H (cpzA3H) in complex with HIV-1 Vif and three components of the CUL5 E3 ligase-CBFβ, EloB, and EloC (VCBC). The structure captures cpzA3H as an RNA-mediated dimer within the cpzA3H-VCBC complex, allowing us to examine the role of dimerization. We find that ubiquitination occurs specifically at two lysine residues on the Vif-proximal protomer, while the distal protomer remains unmodified. The structural model of the active cpzA3H-Vif-CUL5 E3 ligase holoenzyme reveals spatial preferences for ubiquitin transfer to the targeted lysine residues. These findings enhance our understanding of A3H degradation and suggest new antiviral strategies targeting this host-virus interface.
胞嘧啶脱氨酶的载脂蛋白B mRNA编辑酶催化多肽样 3 家族（APOBEC3 家族）通过使病毒 DNA 发生突变来限制像 HIV-1 这样的逆转录病毒。HIV-1 通过产生 Vif 来逃避这种限制，Vif 会招募Cullin-5（CUL5）E3 泛素连接酶复合物以促进 APOBEC3 的降解。在此，我们通过确定黑猩猩 APOBEC3H（cpzA3H）与 HIV-1 Vif 以及 CUL5 E3 连接酶的三个组分——CBFβ、EloB 和 EloC（VCBC）形成的复合物的 3.6 埃冷冻电镜结构，解析了这种反防御机制的关键方面。该结构捕捉到 cpzA3H 在 cpzA3H-VCBC 复合物中作为 RNA 介导的二聚体，使我们能够研究二聚化的作用。我们发现泛素化特异性地发生在靠近 Vif 的原聚体上的两个赖氨酸残基处，而远端原聚体保持未修饰状态。活性 cpzA3H-Vif-CUL5 E3 连接酶全酶的结构模型揭示了泛素转移至靶向赖氨酸残基的空间偏好性。这些发现增进了我们对 A3H 降解的理解，并提出了针对这种宿主-病毒界面的新抗病毒策略。
