Evidence map›Paper›PMID 41315256›Full record

ArticleNature communications2025

Visualizing the translation landscape in human cells at high resolution.

Wei Zheng, Yuekang Zhang, Jimin Wang, Shuhui Wang, Pengxin Chai, Elizabeth J Bailey, Chenghao Zhu, Wangbiao Guo, Swapnil C Devarkar, Shenping Wu and 5 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.

0numbers the graph read from it
0cells of the map it votes in
19citing 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

19 citing papers in PubMed.

  1. Article
  2. eLife · 2026
    Article
  3. Review
  4. Review
  5. Review
  6. Review
  7. Article
  8. Article
  9. The molecular architecture of tunneling nanotubes.bioRxiv : the preprint server for biology · 2026
    Article
  10. Article
  11. Review
  12. Article
  13. Review
  14. Article
  15. Article
  16. Article
  17. Structural Basis of TACO1-Mediated Efficient Mitochondrial Translation.bioRxiv : the preprint server for biology · 2025
    Article
  18. Structural insights into the role of eIF3 in translation mediated by the HCV IRES.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  19. TheBiomolecular NMR assignments · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

15 authors.

Wei ZhengDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Yuekang ZhangDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-4690-3825
Jimin WangDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-4504-8038
Shuhui WangDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-2393-9518
Pengxin ChaiDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-9702-978X
Elizabeth J BaileyDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-5877-7224
Chenghao ZhuDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Wangbiao GuoMicrobial Sciences Institute, Yale University, West Haven, CT, USA.ORCID http://orcid.org/0000-0001-5398-4910
Swapnil C DevarkarDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
Shenping WuDepartment of Pharmacology, Yale University, West Haven, CT, USA.
Jianfeng LinDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-5732-1209
Kai ZhangDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-8617-2855
Jun LiuMicrobial Sciences Institute, Yale University, West Haven, CT, USA.ORCID http://orcid.org/0000-0003-3108-6735
Ivan B LomakinDepartment of Dermatology, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-6528-5068
Yong XiongDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. yong.xiong@yale.edu.ORCID http://orcid.org/0000-0001-9625-9313

Funding

Structure-Function Relationships in the Spirochetal Flagellar MotorR01AI087946 · NIAID · YALE UNIVERSITY · PI LIU, JUN · 2010 to 2025
$6.6M
Functional and Structural Analysis of the Dot/Icm Type IVB Secretion MachineR01AI152421 · NIAID · YALE UNIVERSITY · PI LIU, JUN, ROY, CRAIG R. · 2020 to 2024
$2.9M
NIAID NIH HHS R01 AI087946NIAID NIH HHS R01 AI152421Yale University (Yale) Yale discretionary funds to Y.X.
6 · The paper itself

Abstract

Comprehensive in situ structures of macromolecules can transform our understanding of biology and advance human health. Here, we map protein synthesis inside human cells in detail by combining automated cryo-focused ion beam (FIB) milling and in situ single-particle cryo electron microscopy (cryo-EM). With this in situ cryo-EM approach, we resolved a 2.2 Å consensus structure of the human 80S ribosome and unveiled 23 functional states, nearly all better than 3 Å resolution. Compared to in vitro studies, we observed variations in ribosome structures, distinct environments of ion and polyamine binding, and associated proteins such as EDF1 and NACβ that are typically not enriched with purified ribosomes. We also detected additional peptide-related density features on the ribosome and visualized ribosome-ribosome interactions in helical polysomes. Finally, high-resolution structures from cells treated with homoharringtonine and cycloheximide revealed a distinct translational landscape and a spermidine that interacts with cycloheximide at the E site, one of the numerous polyamines that also bind native ribosomes. These results underscore the value of high-resolution in situ studies in the native environment.

Indexed as

Protein BiosynthesisRibosomesCryoelectron MicroscopyCycloheximideHumansPolyribosomesCycloheximide

Identifiers

PMID41315256
PMCPMC12663405

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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 Socratic graph.