Evidence map›Paper›PMID 38081816›Full record

ArticleNature communications2023

Nearly complete structure of bacteriophage DT57C reveals architecture of head-to-tail interface and lateral tail fibers.

Rafael Ayala, Andrey V Moiseenko, Ting-Hua Chen, Eugene E Kulikov, Alla K Golomidova, Philipp S Orekhov, Maya A Street, Olga S Sokolova, Andrey V Letarov, Matthias Wolf

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.

0numbers the graph read from it
0cells of the map it votes in
35citing papers in PubMed
8.7field-weighted citation impact, top 2% of its field
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

35 citing papers in PubMed, 35 citations in OpenAlex.

  1. The Lord of the Rings: Cysteine bonds crosslink the tail of siphovirus.Protein science : a publication of the Protein Society · 2026
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  4. Novel LyticViruses · 2026
    Article
  5. F-Type Pyocin Versus Phage λ Tail: Conserved Hub, Divergent Fibers.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
  6. Viruses · 2026
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  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Article
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  15. Article
  16. Structural atlas ofbioRxiv : the preprint server for biology · 2025
    Article
  17. Article
  18. Article
  19. 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 at 4 institutions in 4 countries.

Rafael Ayala *Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, 904-0495, Onna-son, Okinawa, Japan.ORCID 0000-0002-9332-4623
Andrey V Moiseenko *Faculty of Biology, Lomonosov Moscow State University, 1 Leninskie Gory, Bld. 12, 119234, Moscow, Russia.ORCID 0000-0003-1112-2356
Ting-Hua Chen *Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, 904-0495, Onna-son, Okinawa, Japan.ORCID 0000-0001-8104-0562
Eugene E KulikovFaculty of Biology, Lomonosov Moscow State University, 1 Leninskie Gory, Bld. 12, 119234, Moscow, Russia.
Alla K GolomidovaWinogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 7/2, 60-Letiya Oktyabrya Ave, 117312, Moscow, Russia.
Philipp S OrekhovFaculty of Biology, Shenzhen MSU-BIT University, 1 International University Park Dr, Dayun New Town, Longgang District, Shenzhen, 518172, China.ORCID 0000-0003-4078-4762
Maya A StreetMolecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, 904-0495, Onna-son, Okinawa, Japan.ORCID 0000-0001-5793-5702
Olga S SokolovaFaculty of Biology, Lomonosov Moscow State University, 1 Leninskie Gory, Bld. 12, 119234, Moscow, Russia. sokolova@mail.bio.msu.ru.ORCID 0000-0003-4678-232X
Andrey V LetarovFaculty of Biology, Lomonosov Moscow State University, 1 Leninskie Gory, Bld. 12, 119234, Moscow, Russia. letarov@gmail.com.ORCID 0000-0002-6991-1983
Matthias WolfMolecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, 904-0495, Onna-son, Okinawa, Japan. matthias.wolf@oist.jp.ORCID 0000-0001-8480-0918
Okinawa Institute of Science and Technology Graduate University · JPRussian Academy of Sciences · RULomonosov Moscow State University · RUShenzhen MSU-BIT University

Funding

MEXT | Japan Society for the Promotion of Science (JSPS) 21K20645National Natural Science Foundation of China (National Science Foundation of China) 32250410316Russian Science Foundation (RSF) 21-44-07002
6 · The paper itself

Abstract

The T5 family of viruses are tailed bacteriophages characterized by a long non-contractile tail. The bacteriophage DT57C is closely related to the paradigmal T5 phage, though it recognizes a different receptor (BtuB) and features highly divergent lateral tail fibers (LTF). Considerable portions of T5-like phages remain structurally uncharacterized. Here, we present the structure of DT57C determined by cryo-EM, and an atomic model of the virus, which was further explored using all-atom molecular dynamics simulations. The structure revealed a unique way of LTF attachment assisted by a dodecameric collar protein LtfC, and an unusual composition of the phage neck constructed of three protein rings. The tape measure protein (TMP) is organized within the tail tube in a three-stranded parallel α-helical coiled coil which makes direct contact with the genomic DNA. The presence of the C-terminal fragment of the TMP that remains within the tail tip suggests that the tail tip complex returns to its original state after DNA ejection. Our results provide a complete atomic structure of a T5-like phage, provide insights into the process of DNA ejection as well as a structural basis for the design of engineered phages and future mechanistic studies.

Indexed as

BacteriophagesDNADNA

Identifiers

PMID38081816
PMCPMC10713586
OpenAlexW4389555270

What OpenQuestion holds

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Registered trials

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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.