Evidence map›Paper›PMID 37865089›Full record

ArticleCell2023

De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking.

Zhen Chen, Momoko Shiozaki, Kelsey M Haas, Will M Skinner, Shumei Zhao, Caiying Guo, Benjamin J Polacco, Zhiheng Yu, Nevan J Krogan, Polina V Lishko and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.

0numbers the graph read from it
0cells of the map it votes in
47citing 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

47 citing papers in PubMed.

  1. Review
  2. Review
  3. Thousandfold Expansion Microscopy.bioRxiv : the preprint server for biology · 2026
    Article
  4. Article
  5. Review
  6. Article
  7. Review
  8. Article
  9. Functional Diversity and Emerging Roles of Human NME/NDPK Group II Proteins.International journal of molecular sciences · 2026
    Review
  10. Article
  11. Ligand-driven modulation of chaperone-cochaperone networks shapes proteostasis outcomes.Protein science : a publication of the Protein Society · 2026
    Article
  12. Article
  13. Article
  14. Review
  15. Amyloid-mediated RNA uptake by sperm for embryonic delivery.bioRxiv : the preprint server for biology · 2025
    Article
  16. Review
  17. Article
  18. Article
  19. Review
  20. Article
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

13 authors.

Zhen ChenDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA. Electronic address: zhen.chen@ucsf.edu.
Momoko ShiozakiJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
Kelsey M HaasDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; J. David Gladstone Institutes, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.
Will M SkinnerDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
Shumei ZhaoJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
Caiying GuoJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
Benjamin J PolaccoDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.
Zhiheng YuJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
Nevan J KroganDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; J. David Gladstone Institutes, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.
Polina V LishkoDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
Robyn M KaakeDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; J. David Gladstone Institutes, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.
Ronald D ValeDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA. Electronic address: valer@janelia.hhmi.org.
David A AgardDepartment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA. Electronic address: david@agard.ucsf.edu.

Funding

Structure & Mechanism: microtubule nucleation, centrosomes, phage cytoskeletonR35GM118099 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AGARD, DAVID A. · 2016 to 2022
$3.6M
Acquisition of an electron microscope for high-resolution single particle cryo-EMS10OD021741 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2016 to 2016
$2.0M
Glacios™ Cryo Transmission Electron Microscope with 200 kV XFEG opticsS10OD026881 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2019 to 2019
$1.8M
Regulation of Microtubule-Based MotilityR35GM118106 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI VALE, RONALD D · 2016 to 2020
$1.7M
Linux cluster for near atomic resolution single particle cryo-EMS10OD020054 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2015 to 2015
$456k
Howard Hughes Medical InstituteNIGMS NIH HHS R35 GM118099NIGMS NIH HHS R35 GM118106NIH HHS S10 OD020054NIH HHS S10 OD021741NIH HHS S10 OD026881
6 · The paper itself

Abstract

To understand the molecular mechanisms of cellular pathways, contemporary workflows typically require multiple techniques to identify proteins, track their localization, and determine their structures in vitro. Here, we combined cellular cryoelectron tomography (cryo-ET) and AlphaFold2 modeling to address these questions and understand how mammalian sperm are built in situ. Our cellular cryo-ET and subtomogram averaging provided 6.0-Å reconstructions of axonemal microtubule structures. The well-resolved tertiary structures allowed us to unbiasedly match sperm-specific densities with 21,615 AlphaFold2-predicted protein models of the mouse proteome. We identified Tektin 5, CCDC105, and SPACA9 as novel microtubule-associated proteins. These proteins form an extensive interaction network crosslinking the lumen of axonemal doublet microtubules, suggesting their roles in modulating the mechanical properties of the filaments. Indeed, Tekt5 -/- sperm possess more deformed flagella with 180° bends. Together, our studies presented a cellular visual proteomics workflow and shed light on the in vivo functions of Tektin 5.

Indexed as

ProteomeSpermatozoaAnimalsAxonemeCryoelectron MicroscopyFlagellaMaleMiceMicrotubulesSemenProteomeAlphaFold2 modelingaxonemecellular cryo-ETdoubletmicrotubulemicrotubule inner proteinspermvisual proteomics

Identifiers

PMID37865089
PMCPMC10842264

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

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.