Electron cryo-microscopy of Bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture

  1. Hemanth KN Reddy  Is a corresponding author
  2. Janos Hajdu
  3. Marta Carroni
  4. Martin Svenda  Is a corresponding author
  1. Uppsala University, Sweden
  2. Stockholm University, Sweden

Abstract

Bacteriophage PR772, a member of the Tectiviridae family, has a 70-nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 Å, while the resolution of the protein capsid is 2.3 Å. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T=25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.

Data availability

CryoEM Density maps and atomic models that support the findings of this study have been deposited in the Electron Microscopy Database and the Protein Databank with the accession codes EMD-4461 (Whole particle reconstruction), EMD-4462 (Vertex Complex), EMD-10237 (Localized reconstruction of the penton region), EMD-10238 (Focused Classification of the penton region) and PDB ID 6Q5U (Atomic model of the asymmetric unit).

The following data sets were generated

Article and author information

Author details

  1. Hemanth KN Reddy

    Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
    For correspondence
    hemanth.kumar@icm.uu.se
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4698-8005
  2. Janos Hajdu

    Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  3. Marta Carroni

    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7697-6427
  4. Martin Svenda

    Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
    For correspondence
    Martin.Svenda@icm.uu.se
    Competing interests
    The authors declare that no competing interests exist.

Funding

Vetenskapsrådet (828-2012-108)

  • Janos Hajdu

Vetenskapsrådet (628-2008-1109)

  • Janos Hajdu

Vetenskapsrådet (822-2010-6157)

  • Janos Hajdu

Vetenskapsrådet (822-2012-5260)

  • Janos Hajdu

Knut och Alice Wallenbergs Stiftelse (KAW-2011.081)

  • Janos Hajdu

European Research Council (ERC-291602)

  • Janos Hajdu

Vetenskapsrådet (349-2011-6488)

  • Janos Hajdu

Vetenskapsrådet (2015-06107)

  • Janos Hajdu

European Structural and Investment Funds (CZ.02.1.01/0.0/0.0/15_003/0000447)

  • Janos Hajdu

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Sjors HW Scheres, MRC Laboratory of Molecular Biology, United Kingdom

Publication history

  1. Received: May 15, 2019
  2. Accepted: September 9, 2019
  3. Accepted Manuscript published: September 12, 2019 (version 1)
  4. Version of Record published: September 18, 2019 (version 2)

Copyright

© 2019, Reddy et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Hemanth KN Reddy
  2. Janos Hajdu
  3. Marta Carroni
  4. Martin Svenda
(2019)
Electron cryo-microscopy of Bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture
eLife 8:e48496.
https://doi.org/10.7554/eLife.48496
  1. Further reading

Further reading

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    Research Article

    Background:

    Ageing is a heterogenous process characterised by cellular and molecular hallmarks, including changes to haematopoietic stem cells and is a primary risk factor for chronic diseases. X chromosome inactivation (XCI) randomly transcriptionally silences either the maternal or paternal X in each cell of 46, XX females to balance the gene expression with 46, XY males. Age acquired XCI-skew describes the preferential selection of cells across a tissue resulting in an imbalance of XCI, which is particularly prevalent in blood tissues of ageing females, and yet its clinical consequences are unknown.

    Methods:

    We assayed XCI in 1575 females from the TwinsUK population cohort using DNA extracted from whole blood. We employed prospective, cross-sectional, and intra-twin study designs to characterise the relationship of XCI-skew with molecular and cellular measures of ageing, cardiovascular disease risk, and cancer diagnosis.

    Results:

    We demonstrate that XCI-skew is independent of traditional markers of biological ageing and is associated with a haematopoietic bias towards the myeloid lineage. Using an atherosclerotic cardiovascular disease risk score, which captures traditional risk factors, XCI-skew is associated with an increased cardiovascular disease risk both cross-sectionally and within XCI-skew discordant twin pairs. In a prospective 10 year follow-up study, XCI-skew is predictive of future cancer incidence.

    Conclusions:

    Our study demonstrates that age acquired XCI-skew captures changes to the haematopoietic stem cell population and has clinical potential as a unique biomarker of chronic disease risk.

    Funding:

    KSS acknowledges funding from the Medical Research Council [MR/M004422/1 and MR/R023131/1]. JTB acknowledges funding from the ESRC [ES/N000404/1]. MM acknowledges funding from the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London. TwinsUK is funded by the Wellcome Trust, Medical Research Council, European Union, Chronic Disease Research Foundation (CDRF), Zoe Global Ltd and the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London.