Evidence map›Paper›PMID 29038566›Full record

ArticleScientific reports2017

Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy.

Kenta Okamoto, Naoyuki Miyazaki, Chihong Song, Filipe R N C Maia, Hemanth K N Reddy, Chantal Abergel, Jean-Michel Claverie, Janos Hajdu, Martin Svenda, Kazuyoshi Murata

Abstract read
In one paragraph

Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

17 citing papers in PubMed.

  1. Article
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  5. Article
  6. Review
  7. Quantitative Cryo-Electron Tomography.Frontiers in molecular biosciences · 2022
    Review
  8. Article
  9. Article
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  11. Review
  12. Review
  13. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Kenta OkamotoLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden. kenta.okamoto@icm.uu.se.
Naoyuki MiyazakiNational Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585, Japan.
Chihong SongNational Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585, Japan.
Filipe R N C MaiaLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.
Hemanth K N ReddyLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.
Chantal AbergelStructural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, 13288, France.ORCID 0000-0003-1875-4049
Jean-Michel ClaverieStructural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, 13288, France.
Janos HajduLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.
Martin SvendaLaboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.
Kazuyoshi MurataNational Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585, Japan. kazum@nips.ac.jp.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The Pithoviridae giant virus family exhibits the largest viral particle known so far, a prolate spheroid up to 2.5 μm in length and 0.9 μm in diameter. These particles show significant variations in size. Little is known about the structure of the intact virion due to technical limitations with conventional electron cryo-microscopy (cryo-EM) when imaging thick specimens. Here we present the intact structure of the giant Pithovirus sibericum particle at near native conditions using high-voltage electron cryo-tomography (cryo-ET) and energy-filtered cryo-EM. We detected a previously undescribed low-density outer layer covering the tegument and a periodical structuring of the fibres in the striated apical cork. Energy-filtered Zernike phase-contrast cryo-EM images show distinct substructures inside the particles, implicating an internal compartmentalisation. The density of the interior volume of Pithovirus particles is three quarters lower than that of the Mimivirus. However, it is remarkably high given that the 600 kbp Pithovirus genome is only half the size of the Mimivirus genome and is packaged in a volume up to 100 times larger. These observations suggest that the interior is densely packed with macromolecules in addition to the genomic nucleic acid.

Indexed as

Cryoelectron MicroscopyElectron Microscope TomographyImaging, Three-DimensionalVirionViruses

Identifiers

PMID29038566
PMCPMC5643343

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.