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Resolving endogenous protein organization in cells with nanometer resolution.

Overview

Authors: Janna Eilts1, Marvin Jungblut2, Dominic A Helmerich1, Stefan Sachs1, Christian Werner1, Cristian-Alexandru Bogaciu3, Ali H Shaib3, Silvio O Rizzoli3, Philip Kollmannsberger1, Sören Doose1, Markus Sauer1,2
ORCID iDs: Janna Eilts, Dominic A Helmerich, Christian Werner, Ali H Shaib, Silvio O Rizzoli, Sören Doose, Markus Sauer
  1. Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
  2. Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
  3. Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
Institutions: University of Würzburg (Germany); Universitätsmedizin Göttingen (Germany)
Journal: Nature communications, volume 17, issue 1, article 7583
Dates: received 8 June 2026; accepted 21 July 2026; published online 29 July 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41467-026-76146-7 · PMID 42527404 · PMCID PMC13421506 · OpenAlex W7171645779
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: histology / microscopy (modality), human (organism), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Statistics, Preprocessing, Machine learning, fMRI & imaging
Keywords: Nanoscale biophysics, Single-molecule biophysics
MeSH: Multiprotein Complexes*, Animals, Humans, Hydrogels, Microscopy, Fluorescence, Microtubules, Nerve Tissue Proteins, Neurons, Tubulin (* major topic)
Topic: Advanced Fluorescence Microscopy Techniques (Biophysics, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: European Research Council (835102)
Citations: cited by 1 paper (Europe PMC); 70 references in the paper

Abstract

Latest refinements in super-resolution microscopy achieved spatial resolutions in the one nanometer range. However, improvement of localization precision advanced faster than labeling methods impeding the translation of such high resolutions to cells. Hence, imaging of the nano-architecture of endogenous multiprotein complexes remains challenging. Here we introduce an expansion microscopy (ExM) method using double-homogenized hydrogels that enables direct stochastic optical reconstruction microscopy (dSTORM) of 7-8-fold expanded immunolabeled samples. The ~4-fold increase in labeling density resolves the 8 nm spacing between neighboring α-tubulin molecules in microtubules, the polyhedral lattice of clathrin-coated pits, and provides evidence for the 8 nm periodicity of α/β-tubulin heterodimers. Two-color Ex-dSTORM further reveals the molecular organization of RIM and the synaptic vesicle priming protein Munc13-1 in 44–48 nm ring-like presynaptic structures in neurons. Ex-dSTORM thus enables nanometer-resolution imaging of endogenous multiprotein complexes in genetically unmodified cells, providing a versatile tool for studying molecular organization in physiological contexts.

Reproduced under the paper's license (CC BY), from the paper cited above.

Code

No file of the authors' code could be read here: it is described below, and read at its source.

Zenodo 21290042

License: CC-BY-4.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Size: 2 files
Software Heritage: not checked
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
At the source:

Code availability

The raw data and source code generated in this study have been deposited in the Zenodo database under 10.5281/zenodo.21290042.

Reproduced under the paper's license (CC BY), from the paper cited above.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 0 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data Availability Statement

Source data are provided with this paper. The raw data and source code generated in this study have been deposited in the Zenodo database under 10.5281/zenodo.21290042. Source data are provided with this paper.

The raw data and source code generated in this study have been deposited in the Zenodo database under 10.5281/zenodo.21290042.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 2 keywords, 9 MeSH terms, 1 funder, 69 references.

Cite

This paper

Eilts, J., Jungblut, M., Helmerich, D. A., Sachs, S., Werner, C., Bogaciu, C.-A., Shaib, A. H., Rizzoli, S. O., Kollmannsberger, P., Doose, S., & Sauer, M. (2026). Resolving endogenous protein organization in cells with nanometer resolution. Nature communications, 17(1), 7583. https://doi.org/10.1038/s41467-026-76146-7

BibTeX

@article{eilts2026resolving,
author = {Eilts, Janna and Jungblut, Marvin and Helmerich, Dominic A and Sachs, Stefan and Werner, Christian and Bogaciu, Cristian-Alexandru and Shaib, Ali H and Rizzoli, Silvio O and Kollmannsberger, Philip and Doose, Sören and Sauer, Markus},
title = {{Resolving endogenous protein organization in cells with nanometer resolution}},
journal = {Nature communications},
year = {2026},
month = jul,
volume = {17},
number = {1},
pages = {7583},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-76146-7},
url = {https://doi.org/10.1038/s41467-026-76146-7},
pmid = {42527404},
pmcid = {PMC13421506}
}

RIS

TY - JOUR
AU - Eilts, Janna
AU - Jungblut, Marvin
AU - Helmerich, Dominic A
AU - Sachs, Stefan
AU - Werner, Christian
AU - Bogaciu, Cristian-Alexandru
AU - Shaib, Ali H
AU - Rizzoli, Silvio O
AU - Kollmannsberger, Philip
AU - Doose, Sören
AU - Sauer, Markus
TI - Resolving endogenous protein organization in cells with nanometer resolution
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/07/29
VL - 17
IS - 1
SP - 7583
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-76146-7
UR - https://doi.org/10.1038/s41467-026-76146-7
LA - en
ER -

CSL-JSON

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