Abstract
The molecular mechanism of HIV-1 entry into host cells is governed by dynamic conformational changes to its envelope glycoprotein (Env), which are triggered by the engagement of the host receptor CD4 and coreceptors. Structural insights into these transitions have been advanced by cryo-electron tomography (cryo-ET), resolving Env structures in closed and multifarious open states within native membranes, and by cryo-electron microscopy (cryo-EM), which has provided atomic details of these states. In this study, we determine cryo-EM structures of soluble native-like Env in complex with antibody 3BC315, antibody b12, CD4, or a combination of 3BC315 and b12, capturing previously uncharacterized conformational states. Observing enhanced 3BC315 binding occupancy in the presence of b12, we investigate the cooperativity of these antibodies using mass photometry and neutralization assays. Integrating these states with the literature, we establish a classification framework for symmetric and asymmetric Env states, categorizing by their degree of openness and stepwise structural rearrangements. Our findings refine the mechanistic understanding of HIV-1 Env dynamics and provide a structural roadmap for targeting dynamic Env states to develop more potent vaccines and immunotherapies.
Data availability
The atomic models were deposited to the Protein Data Bank (PDB) under accession codes 9NBT (AMC008-VRC01-35O22), 9NBY (AMC008-PGT121-VRC01-3BC315), 9YQO (AMC008-PGT121-VRC01), 9NC0 (AMC008-b12), 9OAJ (AMC008-CD4), 9NC3 (AMC008-b12-3BC315), 9NC6 (AMC008-3BC315 (2x)), and 9NC8 (AMC008-3BC315 (1x)). The cryo-EM maps were deposited to the Electron Microscopy Data Bank (EMDB) under accession codes EMD-49236 (AMC008-VRC01-35O22), EMD-49238 (AMC008-PGT121-VRC01-3BC315), EMD-73342 (AMC008-PGT121-VRC01), EMD-49239 (AMC008-b12), EMD-70287 (AMC008-CD4), EMD-49240 (AMC008-b12-3BC315), EMD-49241 (AMC008-3BC315 (2x)), and EMD-49242 (AMC008-3BC315 (1x)). PDB entries 1HZH, 1WIO, 4JY4, 4LST, 4TOY, 5CCK, 5I8H, 5VN3, 5VN8, 6CM3, 6MEO, 6NQD, 6U0L, 6U0N, 6VRW, 7LO6, 7LOK, 7SQ1, 7TFN, 7TFO, 8FYJ, 8TO9, 8TR3, 9D8Y, 9D90, and 9D98, used in this study are available in the PDB. EMDB entry EMD-29294, used in this study is available in the EMDB. Source data are provided as a Source Data file. Source data are provided with this paper.
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Acknowledgements
We thank Thomas Klose at the Purdue University Cryo-EM facility and Ruben Diaz Avalos at the La Jolla Institute for their assistance in sample screening and data collection. We thank Boyu Yin for his assistance in mass photometry experiments. This work was funded by W.W. Smith Charitable Foundation grant A2404 (to J.P.), NIH grant U19 AI166916 (to D.B.W. and J.P.). Funding sources were not involved in the design of this study, the collection and analysis of data, the decision to submit, or the preparation of the manuscript.
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J.C. and J.P. conceived experiments. J.C. produced protein samples. J.D. collected cryo-EM data. J.C., J.D., Z.J.L., and J.P. processed the cryo-EM data. J.C. built atomic models. J.C. and Z.J.L. performed mass photometry experiments. S.G. and R.S. performed pseudovirus neutralization assays. J.C. analyzed and interpreted the data. J.C., Z.J.L., and J.P. wrote the manuscript draft. S.G. contributed to the manuscript draft. All authors reviewed and commented on the manuscript. J.P. and D.B.W. supervised the work and acquired funding.
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D.B.W. notes several possible competing interests, which are managed by the Wistar General Council Office COI committee. These include consulting, BOD service, speaking, which can include in-stock or monetary remuneration, and specific SRAs. Inovio Pharmaceuticals (BOD, consultant and SRA); AstraZeneca (speaker/consultant); Geneos (consultant & SRA); and possibly others that are managed by the Wistar COI Committee. D.B.W. is a member of the International Society for Vaccines, AAI, ASGCT, and AAAS, among other scientific societies. He also serves on NIH and NCI study sections and similar activities for other agencies. The remaining authors declare no competing interests.
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Cui, J., Lin, Z.J., Ghosh, S. et al. Conformational landscape of HIV-1 Env from closed to fully open. Nat Commun (2026). https://doi.org/10.1038/s41467-026-69921-z
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DOI: https://doi.org/10.1038/s41467-026-69921-z
