HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation

Nathaniel Talledge; Huixin Yang; Ke Shi; Raffaele Coray; Guichuan Yu; William g. Arndt; Shuyu Meng; Gloria c. Baxter; Luiza m. Mendonça; Daniel Castaño-Díez; Hideki Aihara; Louis m. Mansky; Wei Zhang

doi:10.1016/j.jmb.2023.168143

HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation

Nathaniel Talledge, Huixin Yang, Ke Shi, Raffaele Coray, Guichuan Yu, William g. Arndt, Shuyu Meng, Gloria c. Baxter, Luiza m. Mendonça, Daniel Castaño-Díez, Hideki Aihara, Louis m. Mansky, Wei Zhang

Research output: Contribution to journal › Article › peer-review

Abstract

Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus type 2 (HIV-2) immature particles possess a distinct and extensive Gag lattice morphology. To better understand the nature of the continuously curved hexagonal Gag lattice, we have used the single particle cryo-electron microscopy method to determine the HIV-2 Gag lattice structure for immature virions. The reconstruction map at 5.5 Å resolution revealed a stable, wineglass-shaped Gag hexamer structure with structural features consistent with other lentiviral immature Gag lattice structures. Cryo-electron tomography provided evidence for nearly complete ordered Gag lattice structures in HIV-2 immature particles. We also solved a 1.98 Å resolution crystal structure of the carboxyl-terminal domain (CTD) of the HIV-2 capsid (CA) protein that identified a structured helix 12 supported via an interaction of helix 10 in the absence of the SP1 region of Gag. Residues at the helix 10–12 interface proved critical in maintaining HIV-2 particle release and infectivity. Taken together, our findings provide the first 3D organization of HIV-2 immature Gag lattice and important insights into both HIV Gag lattice stabilization and virus maturation.

Original language	English (US)
Article number	168143
Journal	Journal of Molecular Biology
Volume	435
Issue number	15
DOIs	https://doi.org/10.1016/j.jmb.2023.168143
State	Published - Aug 1 2023

Bibliographical note

Funding Information:
This work is supported by NIH grant R01 AI177264 (to L.M. and W.Z.). Support is also acknowledged from NIH grants R35 GM118047 (to H.A.) and R21 AI148328 (to W.Z. and L.M.). D.C.D. acknowledges the support of the grant 205321/179041 of the Swiss National Science Foundation (SNF), the grant RGP0017/2020 of the Human Frontiers Science Program (HFSP), and funding from the project PID2021-127309NB-I00 funded by AEI/10 .13039/501100011033/ FEDER, UE. This research was, in part, supported by the National Cancer Institute’s National Cryo-EM Facility at the Frederick National Laboratory for Cancer Research under contract HSSN261200800001E. Parts of this work were carried out in the Characterization Facility, University of Minnesota, which receives partial support from the NSF through the MRSEC (Award Number DMR-2011401 ) and the NNCI (Award Number ECCS-2025124 ) programs. Cryo-ET data collection of HIV-2 MIG construct, and mutants were carried out by Dr. Xiaofeng Fu at the Biological Science Imaging Resource at Florida State University through the U24 GM116788 program. X-ray diffraction data were collected at the Northeastern Collaborative Access Team beamlines, which are funded by NIH ( NIGMS P30 GM124165 ). Cryo-ET StA computations were carried out on the GPU clusters at Minnesota Supercomputing Institute. N.T. was supported by NIH grants T32 DA007097 , F32 AI150351 , and American Cancer Society Postdoctoral Fellowship PF-21-189-01-MPC . W.G.A. was supported by the Institute for Molecular Virology Training Program (i.e., NIH grant T32 AI83196 ).

Funding Information:
This work is supported by NIH grant R01 AI177264 (to L.M. and W.Z.). Support is also acknowledged from NIH grants R35 GM118047 (to H.A.) and R21 AI148328 (to W.Z. and L.M.). D.C.D. acknowledges the support of the grant 205321/179041 of the Swiss National Science Foundation (SNF), the grant RGP0017/2020 of the Human Frontiers Science Program (HFSP), and funding from the project PID2021-127309NB-I00 funded by AEI/10.13039/501100011033/ FEDER, UE. This research was, in part, supported by the National Cancer Institute's National Cryo-EM Facility at the Frederick National Laboratory for Cancer Research under contract HSSN261200800001E. Parts of this work were carried out in the Characterization Facility, University of Minnesota, which receives partial support from the NSF through the MRSEC (Award Number DMR-2011401) and the NNCI (Award Number ECCS-2025124) programs. Cryo-ET data collection of HIV-2 MIG construct, and mutants were carried out by Dr. Xiaofeng Fu at the Biological Science Imaging Resource at Florida State University through the U24 GM116788 program. X-ray diffraction data were collected at the Northeastern Collaborative Access Team beamlines, which are funded by NIH (NIGMS P30 GM124165). Cryo-ET StA computations were carried out on the GPU clusters at Minnesota Supercomputing Institute. N.T. was supported by NIH grants T32 DA007097, F32 AI150351, and American Cancer Society Postdoctoral Fellowship PF-21-189-01-MPC. W.G.A. was supported by the Institute for Molecular Virology Training Program (i.e. NIH grant T32 AI83196). L.M. and W.Z. designed the research. N.T. and L.M. Mendonça purified the immature HIV-2 particles. N.T. performed cryo-EM and cryo-ET reconstructions. K.S. and H.A. solved the crystal structure of HIV-2 CACTD. H.Y. S.M. and W.G.A. performed mutagenesis studies. H.Y. and G.C.B. analyzed production and performed infectivity assays of HIV-2 WT and mutant viruses. H.Y. and S.M. produced mutant viruses for cryo-EM examination. N.T. and W.Z. imaged the WT and mutant virus samples by cryo-EM. W.Z. R.C. and D.C.D. analyzed the Gag lattice structure by the cryo-ET StA method. R.C. and D.C.D. computed the surface coverage of Gag lattices using the DBSCAN and neighborhood analysis methods. G.Y. wrote several imaging processing and analysis programs that enhanced quality and efficiency of the computation. N.T. and K.S. performed structural modeling and fitting. All authors contributed to either drafting and/or revising the paper.

Publisher Copyright:
© 2023 Elsevier Ltd

Keywords

cryo-electron microscopy
lentivirus
morphology
retrovirus
virus assembly

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Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

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This output contributes to the following UN Sustainable Development Goals (SDGs)

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Talledge, N., Yang, H., Shi, K., Coray, R., Yu, G., Arndt, W. G., Meng, S., Baxter, G. C., Mendonça, L. M., Castaño-Díez, D., Aihara, H., Mansky, L. M., & Zhang, W. (2023). HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation. Journal of Molecular Biology, 435(15), Article 168143. https://doi.org/10.1016/j.jmb.2023.168143

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title = "HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation",

abstract = "Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus type 2 (HIV-2) immature particles possess a distinct and extensive Gag lattice morphology. To better understand the nature of the continuously curved hexagonal Gag lattice, we have used the single particle cryo-electron microscopy method to determine the HIV-2 Gag lattice structure for immature virions. The reconstruction map at 5.5 {\AA} resolution revealed a stable, wineglass-shaped Gag hexamer structure with structural features consistent with other lentiviral immature Gag lattice structures. Cryo-electron tomography provided evidence for nearly complete ordered Gag lattice structures in HIV-2 immature particles. We also solved a 1.98 {\AA} resolution crystal structure of the carboxyl-terminal domain (CTD) of the HIV-2 capsid (CA) protein that identified a structured helix 12 supported via an interaction of helix 10 in the absence of the SP1 region of Gag. Residues at the helix 10–12 interface proved critical in maintaining HIV-2 particle release and infectivity. Taken together, our findings provide the first 3D organization of HIV-2 immature Gag lattice and important insights into both HIV Gag lattice stabilization and virus maturation.",

keywords = "cryo-electron microscopy, lentivirus, morphology, retrovirus, virus assembly",

author = "Nathaniel Talledge and Huixin Yang and Ke Shi and Raffaele Coray and Guichuan Yu and Arndt, {William g.} and Shuyu Meng and Baxter, {Gloria c.} and Mendon{\c c}a, {Luiza m.} and Daniel Casta{\~n}o-D{\'i}ez and Hideki Aihara and Mansky, {Louis m.} and Wei Zhang",

note = "Funding Information: This work is supported by NIH grant R01 AI177264 (to L.M. and W.Z.). Support is also acknowledged from NIH grants R35 GM118047 (to H.A.) and R21 AI148328 (to W.Z. and L.M.). D.C.D. acknowledges the support of the grant 205321/179041 of the Swiss National Science Foundation (SNF), the grant RGP0017/2020 of the Human Frontiers Science Program (HFSP), and funding from the project PID2021-127309NB-I00 funded by AEI/10 .13039/501100011033/ FEDER, UE. This research was, in part, supported by the National Cancer Institute{\textquoteright}s National Cryo-EM Facility at the Frederick National Laboratory for Cancer Research under contract HSSN261200800001E. Parts of this work were carried out in the Characterization Facility, University of Minnesota, which receives partial support from the NSF through the MRSEC (Award Number DMR-2011401 ) and the NNCI (Award Number ECCS-2025124 ) programs. Cryo-ET data collection of HIV-2 MIG construct, and mutants were carried out by Dr. Xiaofeng Fu at the Biological Science Imaging Resource at Florida State University through the U24 GM116788 program. X-ray diffraction data were collected at the Northeastern Collaborative Access Team beamlines, which are funded by NIH ( NIGMS P30 GM124165 ). Cryo-ET StA computations were carried out on the GPU clusters at Minnesota Supercomputing Institute. N.T. was supported by NIH grants T32 DA007097 , F32 AI150351 , and American Cancer Society Postdoctoral Fellowship PF-21-189-01-MPC . W.G.A. was supported by the Institute for Molecular Virology Training Program (i.e., NIH grant T32 AI83196 ). Funding Information: This work is supported by NIH grant R01 AI177264 (to L.M. and W.Z.). Support is also acknowledged from NIH grants R35 GM118047 (to H.A.) and R21 AI148328 (to W.Z. and L.M.). D.C.D. acknowledges the support of the grant 205321/179041 of the Swiss National Science Foundation (SNF), the grant RGP0017/2020 of the Human Frontiers Science Program (HFSP), and funding from the project PID2021-127309NB-I00 funded by AEI/10.13039/501100011033/ FEDER, UE. This research was, in part, supported by the National Cancer Institute's National Cryo-EM Facility at the Frederick National Laboratory for Cancer Research under contract HSSN261200800001E. Parts of this work were carried out in the Characterization Facility, University of Minnesota, which receives partial support from the NSF through the MRSEC (Award Number DMR-2011401) and the NNCI (Award Number ECCS-2025124) programs. Cryo-ET data collection of HIV-2 MIG construct, and mutants were carried out by Dr. Xiaofeng Fu at the Biological Science Imaging Resource at Florida State University through the U24 GM116788 program. X-ray diffraction data were collected at the Northeastern Collaborative Access Team beamlines, which are funded by NIH (NIGMS P30 GM124165). Cryo-ET StA computations were carried out on the GPU clusters at Minnesota Supercomputing Institute. N.T. was supported by NIH grants T32 DA007097, F32 AI150351, and American Cancer Society Postdoctoral Fellowship PF-21-189-01-MPC. W.G.A. was supported by the Institute for Molecular Virology Training Program (i.e. NIH grant T32 AI83196). L.M. and W.Z. designed the research. N.T. and L.M. Mendon{\c c}a purified the immature HIV-2 particles. N.T. performed cryo-EM and cryo-ET reconstructions. K.S. and H.A. solved the crystal structure of HIV-2 CACTD. H.Y. S.M. and W.G.A. performed mutagenesis studies. H.Y. and G.C.B. analyzed production and performed infectivity assays of HIV-2 WT and mutant viruses. H.Y. and S.M. produced mutant viruses for cryo-EM examination. N.T. and W.Z. imaged the WT and mutant virus samples by cryo-EM. W.Z. R.C. and D.C.D. analyzed the Gag lattice structure by the cryo-ET StA method. R.C. and D.C.D. computed the surface coverage of Gag lattices using the DBSCAN and neighborhood analysis methods. G.Y. wrote several imaging processing and analysis programs that enhanced quality and efficiency of the computation. N.T. and K.S. performed structural modeling and fitting. All authors contributed to either drafting and/or revising the paper. Publisher Copyright: {\textcopyright} 2023 Elsevier Ltd",

year = "2023",

month = aug,

day = "1",

doi = "10.1016/j.jmb.2023.168143",

language = "English (US)",

volume = "435",

journal = "Journal of Molecular Biology",

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T1 - HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation

AU - Talledge, Nathaniel

AU - Yang, Huixin

AU - Shi, Ke

AU - Coray, Raffaele

AU - Yu, Guichuan

AU - Arndt, William g.

AU - Meng, Shuyu

AU - Baxter, Gloria c.

AU - Mendonça, Luiza m.

AU - Castaño-Díez, Daniel

AU - Aihara, Hideki

AU - Mansky, Louis m.

AU - Zhang, Wei

N1 - Funding Information: This work is supported by NIH grant R01 AI177264 (to L.M. and W.Z.). Support is also acknowledged from NIH grants R35 GM118047 (to H.A.) and R21 AI148328 (to W.Z. and L.M.). D.C.D. acknowledges the support of the grant 205321/179041 of the Swiss National Science Foundation (SNF), the grant RGP0017/2020 of the Human Frontiers Science Program (HFSP), and funding from the project PID2021-127309NB-I00 funded by AEI/10 .13039/501100011033/ FEDER, UE. This research was, in part, supported by the National Cancer Institute’s National Cryo-EM Facility at the Frederick National Laboratory for Cancer Research under contract HSSN261200800001E. Parts of this work were carried out in the Characterization Facility, University of Minnesota, which receives partial support from the NSF through the MRSEC (Award Number DMR-2011401 ) and the NNCI (Award Number ECCS-2025124 ) programs. Cryo-ET data collection of HIV-2 MIG construct, and mutants were carried out by Dr. Xiaofeng Fu at the Biological Science Imaging Resource at Florida State University through the U24 GM116788 program. X-ray diffraction data were collected at the Northeastern Collaborative Access Team beamlines, which are funded by NIH ( NIGMS P30 GM124165 ). Cryo-ET StA computations were carried out on the GPU clusters at Minnesota Supercomputing Institute. N.T. was supported by NIH grants T32 DA007097 , F32 AI150351 , and American Cancer Society Postdoctoral Fellowship PF-21-189-01-MPC . W.G.A. was supported by the Institute for Molecular Virology Training Program (i.e., NIH grant T32 AI83196 ). Funding Information: This work is supported by NIH grant R01 AI177264 (to L.M. and W.Z.). Support is also acknowledged from NIH grants R35 GM118047 (to H.A.) and R21 AI148328 (to W.Z. and L.M.). D.C.D. acknowledges the support of the grant 205321/179041 of the Swiss National Science Foundation (SNF), the grant RGP0017/2020 of the Human Frontiers Science Program (HFSP), and funding from the project PID2021-127309NB-I00 funded by AEI/10.13039/501100011033/ FEDER, UE. This research was, in part, supported by the National Cancer Institute's National Cryo-EM Facility at the Frederick National Laboratory for Cancer Research under contract HSSN261200800001E. Parts of this work were carried out in the Characterization Facility, University of Minnesota, which receives partial support from the NSF through the MRSEC (Award Number DMR-2011401) and the NNCI (Award Number ECCS-2025124) programs. Cryo-ET data collection of HIV-2 MIG construct, and mutants were carried out by Dr. Xiaofeng Fu at the Biological Science Imaging Resource at Florida State University through the U24 GM116788 program. X-ray diffraction data were collected at the Northeastern Collaborative Access Team beamlines, which are funded by NIH (NIGMS P30 GM124165). Cryo-ET StA computations were carried out on the GPU clusters at Minnesota Supercomputing Institute. N.T. was supported by NIH grants T32 DA007097, F32 AI150351, and American Cancer Society Postdoctoral Fellowship PF-21-189-01-MPC. W.G.A. was supported by the Institute for Molecular Virology Training Program (i.e. NIH grant T32 AI83196). L.M. and W.Z. designed the research. N.T. and L.M. Mendonça purified the immature HIV-2 particles. N.T. performed cryo-EM and cryo-ET reconstructions. K.S. and H.A. solved the crystal structure of HIV-2 CACTD. H.Y. S.M. and W.G.A. performed mutagenesis studies. H.Y. and G.C.B. analyzed production and performed infectivity assays of HIV-2 WT and mutant viruses. H.Y. and S.M. produced mutant viruses for cryo-EM examination. N.T. and W.Z. imaged the WT and mutant virus samples by cryo-EM. W.Z. R.C. and D.C.D. analyzed the Gag lattice structure by the cryo-ET StA method. R.C. and D.C.D. computed the surface coverage of Gag lattices using the DBSCAN and neighborhood analysis methods. G.Y. wrote several imaging processing and analysis programs that enhanced quality and efficiency of the computation. N.T. and K.S. performed structural modeling and fitting. All authors contributed to either drafting and/or revising the paper. Publisher Copyright: © 2023 Elsevier Ltd

PY - 2023/8/1

Y1 - 2023/8/1

N2 - Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus type 2 (HIV-2) immature particles possess a distinct and extensive Gag lattice morphology. To better understand the nature of the continuously curved hexagonal Gag lattice, we have used the single particle cryo-electron microscopy method to determine the HIV-2 Gag lattice structure for immature virions. The reconstruction map at 5.5 Å resolution revealed a stable, wineglass-shaped Gag hexamer structure with structural features consistent with other lentiviral immature Gag lattice structures. Cryo-electron tomography provided evidence for nearly complete ordered Gag lattice structures in HIV-2 immature particles. We also solved a 1.98 Å resolution crystal structure of the carboxyl-terminal domain (CTD) of the HIV-2 capsid (CA) protein that identified a structured helix 12 supported via an interaction of helix 10 in the absence of the SP1 region of Gag. Residues at the helix 10–12 interface proved critical in maintaining HIV-2 particle release and infectivity. Taken together, our findings provide the first 3D organization of HIV-2 immature Gag lattice and important insights into both HIV Gag lattice stabilization and virus maturation.

AB - Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus type 2 (HIV-2) immature particles possess a distinct and extensive Gag lattice morphology. To better understand the nature of the continuously curved hexagonal Gag lattice, we have used the single particle cryo-electron microscopy method to determine the HIV-2 Gag lattice structure for immature virions. The reconstruction map at 5.5 Å resolution revealed a stable, wineglass-shaped Gag hexamer structure with structural features consistent with other lentiviral immature Gag lattice structures. Cryo-electron tomography provided evidence for nearly complete ordered Gag lattice structures in HIV-2 immature particles. We also solved a 1.98 Å resolution crystal structure of the carboxyl-terminal domain (CTD) of the HIV-2 capsid (CA) protein that identified a structured helix 12 supported via an interaction of helix 10 in the absence of the SP1 region of Gag. Residues at the helix 10–12 interface proved critical in maintaining HIV-2 particle release and infectivity. Taken together, our findings provide the first 3D organization of HIV-2 immature Gag lattice and important insights into both HIV Gag lattice stabilization and virus maturation.

KW - cryo-electron microscopy

KW - lentivirus

KW - morphology

KW - retrovirus

KW - virus assembly

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HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation

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HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation

Abstract

Bibliographical note

Keywords

MRSEC Support

PubMed: MeSH publication types

UN SDGs

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