# Comprehensive Insights into the Molecular Basis of HIV Glycoprotein
## 2 Proteins Engaged in HIV Entry
### Env/gp160
#### 2.1.2 Structural Characteristics of Env/gp160  
The full-length Env protein consists of several critical components essential for viral infectivity: a spike-shaped glycosylated ectodomain, a trimerized single-pass TMD, and a highly conserved membrane-proximal external region (MPER). Additionally, it features a membrane-interacting amphipathic CT composed of approximately 150 amino acid residues (Figure 2a). Each of these regions plays a pivotal role in the structural integrity and functionality of the Env protein during the HIV-1 infection process [28; 59; 60; 61]. The membrane protein spikes of HIV-1 Env have been challenging to analyze at high resolution for an extended period. Currently, HIV-1 Env spike proteins have only been visualized at relatively low resolution (\(\sim\)20 A) using cryo-electron tomography (cryo-ET) [62; 63]. The trimeric soluble ectodomain Env, SOSIP.664, has been derived from the BG505 isolate of clade A HIV-1 since 2013. This construct includes several specific modifications: isoleucine to proline substitution at residue 559, a disulfide bond that crosslinks gp120 and gp41, and a truncation at residue 664. These alterations enhance the stability and mimic the native structure of the Env protein, making SOSIP.664 a valuable tool in HIV-1 research and vaccine development [64]. The intriguing finding from a study reveals the loss of viral infectivity after the SOSIP modifications [65]. Figure 3a-c shows the structures of BG505 clade A SOSIP.664 and JR-FL Env\(\Delta\)CT clade B HIV-1, elucidated through X-ray crystallography (XRC) and cryo-electron microscopy (EM), respectively. This comparison sheds light on the structural alterations induced by these modifications and their implications for viral functionality [22; 66; 67]. The trimeric molecular structures of Env represent distinct prefusion and postfusion states of gp41. They capture the prefusion conformation of gp41 before membrane fusion and the postfusion six-helix bundle configuration after fusion. This distinction is crucial for understanding the dynamic changes that Env undergoes during the viral entry process [22]. In previous studies, the TMD of the Env protein was not typically considered for its role in passive membrane anchoring. However, research has begun investigating the TMDs of HIV-1 Env proteins and their neighboring regions within the lipid bilayer context. Consequently, many HIV-1 Env proteins expressed on human cell surfaces display conformational uniformity, including those derived from challenging-to-neutralize primary isolates of HIV-1. This finding expanded understanding and underscores the importance of considering the entire Env protein structure, including its membrane-interacting regions, for comprehensive analysis and potential therapeutic targeting [68; 69]. Antigencity plays a crucial role in antibody neutralization, where epitopes exposed on the HIV-1 Env are targeted by broadly neutralizing antibodies, while others remain concealed from non-neutralizing antibodies. The truncation of the CT of these uniform Envs causes the loss of fusogenic activity. However, it also leads to the exposure of previously hidden non-neutralizing epitopes on both gp120 and gp41. This alteration highlights the intricate relationship between Env structure, antigenicity, and antibody recognition, providing insights into potential strategies for vaccine design and therapeutic intervention [68]. The extended CT of approximately 150 residues in the Env membrane represents a notable characteristic facilitating its efficient incorporation into virions [28]. Truncation of CTs in specific HIV-1 isolates has been observed to have a minimal impact on the antigenicity of the Env protein [70; 71]. In this context, the CT unexpectedly influences the conformational variability of the Env ectodomain by interacting with the TMD. An NMR analysis effectively reconstituted the TMD within bicelles, providing a model mimicking the lipid bilayer environment.