Nanobodies can achieve remarkable neutralization of genetically diverse pathogens, including HIV-1. To gain insight into their recognition, we determined crystal structures of four llama nanobodies (J3, A12, C8, and D7), all of which targeted the CD4-binding site, in complex with the HIV-1 envelope (Env) gp120 core, and determined a cryoelectron microscopy (cryo-EM) structure of J3 with the Env trimer. Crystal and cryo-EM structures of J3 complexes revealed this nanobody to mimic binding to the prefusion-closed trimer for the primary site of CD4 recognition as well as a secondary quaternary site. In contrast, crystal structures of A12, C8, and D7 with gp120 revealed epitopes that included portions of the gp120 inner domain, inaccessible on the prefusion-closed trimer. Overall, these structures explain the broad and potent neutralization of J3 and limited neutralization of A12, C8, and D7, which utilized binding modes incompatible with the neutralization-targeted prefusion-closed conformation of Env.

纳米抗体可以显着中和遗传多样性的病原体，包括 HIV-1。为了深入了解它们的识别，我们确定了四种美洲驼纳米抗体（J3、A12、C8 和 D7）的晶体结构，所有这些纳米抗体都靶向 CD4 结合位点，与 HIV-1 包膜 (Env) gp120 核心复合，并用 Env 三聚体确定了 J3 的低温电子显微镜 (cryo-EM) 结构。J3 复合物的晶体和低温 EM 结构揭示了该纳米抗体模拟与 CD4 识别主要位点以及次级四元位点的融合前闭合三聚体的结合。相比之下，具有 gp120 的 A12、C8 和 D7 的晶体结构揭示了包含 gp120 内部结构域部分的表位，这些表位在预融合闭合三聚体上不可接近。全面的，