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Molecular architecture and conservation of an immature human endogenous retrovirus

Author

Listed:
  • Anna-Sophia Krebs

    (Wellcome Trust Centre for Human Genetics, University of Oxford)

  • Hsuan-Fu Liu

    (Duke University School of Medicine)

  • Ye Zhou

    (Duke University)

  • Juan S. Rey

    (University of Delaware)

  • Lev Levintov

    (University of Delaware)

  • Juan Shen

    (Wellcome Trust Centre for Human Genetics, University of Oxford)

  • Andrew Howe

    (Diamond Light Source, Harwell Science and Innovation Campus)

  • Juan R. Perilla

    (University of Delaware)

  • Alberto Bartesaghi

    (Duke University School of Medicine
    Duke University
    Duke University)

  • Peijun Zhang

    (Wellcome Trust Centre for Human Genetics, University of Oxford
    Diamond Light Source, Harwell Science and Innovation Campus
    Chinese Academy of Medical Sciences Oxford Institute, University of Oxford)

Abstract

The human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus in the human genome and is activated and expressed in many cancers and amyotrophic lateral sclerosis. We present the immature HERV-K capsid structure at 3.2 Å resolution determined from native virus-like particles using cryo-electron tomography and subtomogram averaging. The structure shows a hexamer unit oligomerized through a 6-helix bundle, which is stabilized by a small molecule analogous to IP6 in immature HIV-1 capsid. The HERV-K immature lattice is assembled via highly conserved dimer and trimer interfaces, as detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the linker between the N-terminal and the C-terminal domains of CA occurs during HERV-K maturation. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time.

Suggested Citation

  • Anna-Sophia Krebs & Hsuan-Fu Liu & Ye Zhou & Juan S. Rey & Lev Levintov & Juan Shen & Andrew Howe & Juan R. Perilla & Alberto Bartesaghi & Peijun Zhang, 2023. "Molecular architecture and conservation of an immature human endogenous retrovirus," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40786-w
    DOI: 10.1038/s41467-023-40786-w
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    as
    1. Robert A. Dick & Kaneil K. Zadrozny & Chaoyi Xu & Florian K. M. Schur & Terri D. Lyddon & Clifton L. Ricana & Jonathan M. Wagner & Juan R. Perilla & Barbie K. Ganser-Pornillos & Marc C. Johnson & Owen, 2018. "Inositol phosphates are assembly co-factors for HIV-1," Nature, Nature, vol. 560(7719), pages 509-512, August.
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    3. Martin Obr & Clifton L. Ricana & Nadia Nikulin & Jon-Philip R. Feathers & Marco Klanschnig & Andreas Thader & Marc C. Johnson & Volker M. Vogt & Florian K. M. Schur & Robert A. Dick, 2021. "Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    4. Robert A. Dick & Kaneil K. Zadrozny & Chaoyi Xu & Florian K. M. Schur & Terri D. Lyddon & Clifton L. Ricana & Jonathan M. Wagner & Juan R. Perilla & Barbie K. Ganser-Pornillos & Marc C. Johnson & Owen, 2018. "Author Correction: Inositol phosphates are assembly co-factors for HIV-1," Nature, Nature, vol. 563(7731), pages 22-22, November.
    5. Jiying Ning & Gonca Erdemci-Tandogan & Ernest L. Yufenyuy & Jef Wagner & Benjamin A. Himes & Gongpu Zhao & Christopher Aiken & Roya Zandi & Peijun Zhang, 2016. "In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway," Nature Communications, Nature, vol. 7(1), pages 1-12, December.
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