Evidence map›Paper›PMID 39127037›Full record

ArticleCell2024

The molecular architecture of the nuclear basket.

Digvijay Singh, Neelesh Soni, Joshua Hutchings, Ignacia Echeverria, Farhaz Shaikh, Madeleine Duquette, Sergey Suslov, Zhixun Li, Trevor van Eeuwen, Kelly Molloy and 8 more

Abstract read
In one paragraph

Article in Cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.

0numbers the graph read from it
0cells of the map it votes in
56citing 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

56 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. Article
  5. Article
  6. HIV-1 capsid interactions with Nuclear Pore Complex components support nuclear entry via affinity gradient.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. MolViewStories: Interactive molecular storytelling.Protein science : a publication of the Protein Society · 2026
    Article
  14. Article
  15. Review
  16. Review
  17. bioRxiv : the preprint server for biology · 2026
    Article
  18. Vascular Mechanobiology: From Membrane to Nucleus.Advances in experimental medicine and biology · 2026
    Review
  19. Review
  20. Structure, function and assembly of nuclear pore complexes.Nature reviews. Molecular cell biology · 2026
    Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

18 authors.

Digvijay SinghSchool of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
Neelesh SoniDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
Joshua HutchingsSchool of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
Ignacia EcheverriaDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
Farhaz ShaikhSchool of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
Madeleine DuquetteSchool of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
Sergey SuslovSchool of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
Zhixun LiState Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P.R. China.
Trevor van EeuwenLaboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
Kelly MolloyLaboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
Yi ShiLaboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
Junjie WangLaboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
Qiang GuoState Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P.R. China.
Brian T ChaitLaboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
Javier Fernandez-MartinezLaboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain; Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain. Electronic address: javier.fernandezma@ehu.eus.
Michael P RoutLaboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address: rout@rockefeller.edu.
Andrej SaliDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: sali@salilab.org.
Elizabeth VillaSchool of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: evilla@ucsd.edu.

Funding

CHEETAH Center for the Structural Biology of HIV Infection, Restriction, and Viral DynamicsU54AI170856 · NIAID · UTAH STATE HIGHER EDUCATION SYSTEM--UNIVERSITY OF UTAH · PI Pamela J Bjorkman · 2022 to 2026
$34.4M
TR&D Project 4. The Imaging Stage: Multiscale Spatiotemporal Modeling of Macromolecular Systems in Cellular NeighborhoodsP41GM109824 · NIGMS · ROCKEFELLER UNIVERSITY · PI ROUT, MICHAEL P · 2014 to 2023
$18.8M
Pathways in Biological Sciences Training ProgramT32GM133351 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Matthew Daugherty, Randolph Y. Hampton · 2020 to 2026
$9.9M
Structure-Function Mapping of the Nuclear Pore Complex-RenewalR01GM112108 · NIGMS · ROCKEFELLER UNIVERSITY · PI JOHN D. AITCHISON, MICHAEL P ROUT · 2015 to 2026
$9.1M
IMP: Software for Hybrid Determination of Macromolecular Assembly StructuresR01GM083960 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2008 to 2024
$5.2M
Molecular and cellular biology of the phage nucleus and spindleR01GM129245 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI POGLIANO, JOSEPH A · 2018 to 2025
$4.2M
The dynamic mechanism of nuclear transport visualized at the atomic scaleR01GM117212 · NIGMS · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI COWBURN, DAVID · 2016 to 2023
$3.7M
Mapping the Dynamic Interactome of Ig-fold Membrane Proteins Using Nanobody-Based ToolsR35GM137905 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Yi Shi · 2020 to 2026
$2.8M
In situ imaging of the aging-induced structural and stoichiometric degradation of the nuclear pore complex and nuclear peripheryK99AG080112 · NIA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SINGH, DIGVIJAY · 2023 to 2024
$213k
NIAID NIH HHS U54 AI170856NIA NIH HHS K99 AG080112NIGMS NIH HHS P41 GM109824NIGMS NIH HHS R01 GM083960NIGMS NIH HHS R01 GM112108NIGMS NIH HHS R01 GM117212NIGMS NIH HHS R01 GM129245NIGMS NIH HHS R35 GM137905NIGMS NIH HHS T32 GM133351
6 · The paper itself

Abstract

The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of nucleoporins (Nups) in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.

Indexed as

Active Transport, Cell NucleusNuclear PoreNuclear Pore Complex ProteinsSaccharomyces cerevisiaeAnimalsCell NucleusCryoelectron MicroscopyMiceModels, MolecularRNA, MessengerSaccharomyces cerevisiae ProteinsToxoplasmaNuclear Pore Complex ProteinsRNA, MessengerSaccharomyces cerevisiae Proteinschromatin organizationcross-linking mass spectrometrycryo-electron tomographycryo-focused-ion-beam millingin-cell structural biologyintegrative modelingmRNA transportNPCnuclear basketnuclear pore complexsubtomogram analysis

Identifiers

PMID39127037
PMCPMC11416316

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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.