Evidence map›Paper›PMID 39152109›Full record

ArticleNature communications2024

Atomic structures of a bacteriocin targeting Gram-positive bacteria.

Xiaoying Cai, Yao He, Iris Yu, Anthony Imani, Dean Scholl, Jeff F Miller, Z Hong Zhou

Abstract read
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing 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

15 citing papers in PubMed.

  1. F-Type Pyocin Versus Phage λ Tail: Conserved Hub, Divergent Fibers.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
  2. Article
  3. Article
  4. Review
  5. Article
  6. Article
  7. Review
  8. Article
  9. A dramatic protein fold switch powers a bactericidal nanomachine.bioRxiv : the preprint server for biology · 2026
    Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. Article
  15. Gut microbiome: a biomedical revolution.Nature reviews. Gastroenterology & hepatology · 2024
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Xiaoying CaiDepartment of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.ORCID 0000-0001-6694-2154
Yao HeDepartment of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.ORCID 0000-0002-1368-6422
Iris YuDepartment of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
Anthony ImaniDepartment of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
Dean SchollPylum Biosciences, San Francisco, CA, 94080, USA.
Jeff F MillerDepartment of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA. jfmiller@ucla.edu.
Z Hong ZhouDepartment of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA. Hong.Zhou@UCLA.edu.ORCID 0000-0002-8373-4717

Funding

High-Resolution CryoEM Reconstruction of Large ComplexesR01GM071940 · NIGMS · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI ZHOU, Z HONG · 2006 to 2025
$5.0M
In situ atomic structures of the Kaposi's sarcoma-associated herpesvirus portal-terminase complex and glycoproteinsR01DE025567 · NIDCR · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI WU, TING-TING, ZHOU, Z HONG · 2016 to 2024
$4.0M
Structural basis of human cytomegalovirus replication within host cellsR01DE028583 · NIDCR · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Z Hong ZHOU · 2019 to 2026
$3.2M
Title: Development of Modified R-type Bacteriocins to Specifically Target C. difficileand Prevent Relapse of CDIs.R33AI121692 · NIAID · PYLUM BIOSCIENCES, INC. · PI SCHOLL, DEAN M · 2018 to 2020
$1.5M
Direct Detection Device for atomic resolution cryoEM of macromolecular complexesS10OD018111 · OD · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ZHOU, Z HONG · 2014 to 2014
$598k
Generating a library of antimicrobial R-type pyocins against enteric bacteriaR21AI085318 · NIAID · AVIDBIOTICS CORPORATION · PI SCHOLL, DEAN M · 2010 to 2011
$373k
NIAID NIH HHS R21 AI085318NIAID NIH HHS R33 AI121692NIDCR NIH HHS R01 DE025567NIDCR NIH HHS R01 DE028583NIGMS NIH HHS R01 GM071940NIH HHS S10 OD018111U.S. Department of Health & Human Services | National Institutes of Health (NIH) R33AI121692U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR) DE028583U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R01GM071940
6 · The paper itself

Abstract

Due to envelope differences between Gram-positive and Gram-negative bacteria, engineering precision bactericidal contractile nanomachines requires atomic-level understanding of their structures; however, only those killing Gram-negative bacteria are currently known. Here, we report the atomic structures of an engineered diffocin, a contractile syringe-like molecular machine that kills the Gram-positive bacterium Clostridioides difficile. Captured in one pre-contraction and two post-contraction states, each structure fashions six proteins in the bacteria-targeting baseplate, two proteins in the energy-storing trunk, and a collar linking the sheath with the membrane-penetrating tube. Compared to contractile machines targeting Gram-negative bacteria, major differences reside in the baseplate and contraction magnitude, consistent with target envelope differences. The multifunctional hub-hydrolase protein connects the tube and baseplate and is positioned to degrade peptidoglycan during penetration. The full-length tape measure protein forms a coiled-coil helix bundle homotrimer spanning the entire diffocin. Our study offers mechanical insights and principles for designing potent protein-based precision antibiotics.

Indexed as

Anti-Bacterial AgentsBacteriocinsClostridioides difficileBacterial ProteinsCrystallography, X-RayGram-Positive BacteriaModels, MolecularPeptidoglycanAnti-Bacterial AgentsBacterial ProteinsBacteriocinsPeptidoglycan

Identifiers

PMID39152109
PMCPMC11329794

What OpenQuestion holds

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LicenceCC BY
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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.