Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike

Abstract

SUMMARY For many enveloped viruses, binding to a receptor(s) on a host cell acts as a first step in a series of events culminating in fusion with the host cell membrane and transfer of genetic material for replication [for review see1,2]. The envelope glycoprotein (Env) trimer on the surface of HIV is responsible for receptor binding and fusion. While Env can tolerate a high degree of mutation in five variable regions (V1-V5), and also at N-linked glycosylation sites that contribute roughly half the mass of Env, the functional sites for recognition of receptor CD4 and co-receptor CXCR4/CCR5 are conserved and essential for viral fitness. Soluble SOSIP Env trimers are structural and antigenic mimics of the pre-fusion native, surface-presented Env3,4, targets of broadly neutralizing antibodies (bnAbs). Thus, they are attractive immunogens for vaccine development [for review see5–8]. Here we present high-resolution cryo-electron microscopy (cryoEM) structures of subtype B B41 SOSIP Env trimers in complex with CD4 and antibody 17b, or with antibody b12, at resolutions of ~3.7 Å and ~3.6 Å, respectively, and compare them to cryoEM reconstructions of ligand-free B41 SOSIP Env trimers or in complex with either CD4 or CD4bs antibody PGV04, at ~5.6 Å, ~5.2 Å and ~7.4 Å, respectively. Consequently, we present the most complete description and understanding of the CD4/17b-induced intermediate and provide the molecular basis of the receptor-binding induced conformational change required for HIV-1 entry into host cells. Both CD4 and b12 induce large, previously uncharacterized conformational rearrangements in the gp41 subunits, and the fusion peptide becomes more buried in a newly formed pocket. These structures provide key details on the biological function of the type I viral fusion machine from HIV-1 as well as new templates for inhibitor design.

Targeting the Late Stage of HIV-1 Entry for Antibody-Dependent Cellular Cytotoxicity: Structural Basis for Env Epitopes in the C11 Region

“…We and others have shown that soluble CD4 induces a metastable conformation of the trimer in which gp120 protomers are displaced but still remain involved in the gp41 interaction thus incapable of exposure of the A32- and C11-epitope regions (Acharya et al, 2014; Ozorowski et al, 2017; Pancera et al, 2010; Wang et al, 2016). We are able, however, to induce the conformational changes of the viral trimer similar to those induced by cell surface CD4 with the CD4 miniprotein mimetic M48U1 alone or in combination with co-receptor binding site antibody.…”

“…In the pre-fusion trimer, the N- and C- termini of gp120 are held by a triple-tryptophan clasp consisting of tryptophans 623, 628, and 623 of gp41 (Pancera et al, 2014). Upon binding of the Env trimer to the cell surface CD4, the inner domain of gp120 undergoes a series of conformation rearrangements with the formation of the bridging sheet and changes to the region of the nascent N5-i5 epitope (conformation from PDB: 5VN3, (Ozorowski et al, 2017)). In this state, the α0-helix and the -strand of the N5-i5 epitope are formed and the β1 helix is positioned to assume conformation as seen in the N5-i5-bound state.…”

“…This structure confirms that these two epitope regions are non-overlapping and defines new features of the gp120 N-terminus not seen previously. When bound to N12-i3, residues 31–42 of the gp120 N-terminus form an 8 th β-strand to extend the 7-stranded β-sandwich formed by the gp120 inner domain seen in other Env structures including the PGT151-stabilized Env trimer (Lee et al, 2016), the CD4-trigered Env trimer (Ozorowski et al, 2017), and the gp120 core with N- and C-termini (Finzi et al, 2010; Pancera et al, 2010). These results indicate the importance of Epitope Cluster A as a major ADCC target for HIV-1 as well as identifying a new N-terminal structure that is implicated as an intermediate in a late entry state.…”

Designing Molecular Spanners to Throw in the Protein Networks

“…Finally, cryo‐electron microscopy (CryoEM)—emerging as the new powerful structural technique of the moment—is already transforming the way we look into complex biological macromolecules . In this respect, Ozorowski et al . studied the open and closed structures of HIV‐1 envelope glycoprotein (gp120; Env) to reveal allosteric control mechanisms, raising the possibility of using this knowledge for the design of HIV‐1 inhibitors.…”

Cryo-EM Studies of Virus-Antibody Immune Complexes

“…Twenty antibody classes targeting six epitopes on the prefusion closed HIV-1 Env trimer have been characterized using SPA (Table 3) and crystallographic studies (Chuang et al 2019). 'Breathing' by HIV-1 B41 SOSIP.664 trimers was found to expose the b12 epitope (Ozorowski et al 2017), and a similar motion by influenza HA protomers was also revealed by SPA (Turner et al 2019). S230 binding induces fusogenic conformational rearrangements in the SARS-CoV S glycoprotein, while the MERS-CoV S glycoprotein remains its prefusion conformation upon LCA60 binding Walls et al 2019).…”