Journal article
Structure of native HIV-1 cores and their interactions with IP6 and CypA
T Ni, Y Zhu, Z Yang, C Xu, Y Chaban, T Nesterova, J Ning, T Böcking, MW Parker, C Monnie, J Ahn, JR Perilla, P Zhang
Science Advances | Published : 2021
Abstract
The viral capsid plays essential roles in HIV replication and is a major platform engaging host factors. To overcome challenges in study native capsid structure, we used the perfringolysin O to perforate the membrane of HIV-1 particles, thus allowing host proteins and small molecules to access the native capsid while improving cryo-electron microscopy image quality. Using cryo-electron tomography and subtomogram averaging, we determined the structures of native capsomers in the presence and absence of inositol hexakisphosphate (IP6) and cyclophilin A and constructed an all-atom model of a complete HIV-1 capsid. Our structures reveal two IP6 binding sites and modes of cyclophilin A interactio..
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Grants
Awarded by UK Research and Innovation
Funding Acknowledgements
The computational aspects of this research were supported by the Wellcome Trust Core Award grant number 203141/Z/16/Z and the NIHR Oxford BRC. This work was supported by the National Institutes of Health grants P50AI150481, AI129862, AI157843, and P20GM104316; the U. K. Wellcome Trust Investigator Award 206422/Z/17/Z; and the U.K. Biotechnology and Biological Sciences Research Council grant BB/S003339/1. PFO production was supported with an Australian Research Council Discovery Project grant DP160101874. Funding from the Victorian Government Operational Infrastructure Support Scheme to St Vincent's Institute is acknowledged. M.W.P. is a National Health and Medical Research Council of Australia Research Fellow (APP1117183). This work used the Extreme Science and Engineering Discovery Environment, which is supported by the National Science Foundation (grant ACI-1548562). This work used XSEDE Bridges and Stampede2 at the Pittsburgh Super Computing Center and Texas Advanced Computing Center, respectively, through allocation MCB170096. Author contributions: P.Z. conceived the research and designed the experiments. T. Ni purified HIV-1 Env-VLPs. C.M. and J.A. purified CypA and CypA-DsRed proteins. T.B. and M.W.P. advised on the use of PFO. J.N. performed CypA-DsRed and CA tube-binding assays. T. Ni, Y. Z., Z.Y., and Y.C. collected cryoET data. Y.C. performed cryoEM SPA analysis of CypA-DsRed. T. Ni, Y.Z., and Z.Y. performed tomography reconstruction and STA. Y.Z. performed localized classification using emClarity. T. Ni and Y.Z. refined the structural models. C.X. and J.R.P. designed and performed free energy calculations, and T.N. and J.R.P. performed MD all-atom simulation of the capsid. T. Ni, Y.Z., C.X., J.R.P., and P.Z. analyzed data. T. Ni, Y.Z., J.R.P., and P.Z. wrote the paper with support from all the authors.