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Cited by 12Autophagy in Disease and TherapyAdvanced Electron Microscopy Techniques and ApplicationsUbiquitin and proteasome pathways

Structural organization of p62 filaments and the cellular ultrastructure of calcium-rich p62-enwrapped lipid droplet cargo

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Berkamp, Sabrina, Jungbluth, Lisa, Katranidis, Alexandros, Mostafavi, Siavash, Korculanin, Olivera, Lu, Peng-Han, Ickert, Lotte, Dierig, Maya M. +7 more·2025·Nature Communications
DOI 10.1038/s41467-025-66785-7PMC PMC12669770

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Abstract

The selective autophagy receptor p62/SQSTM1 is known to form higher-order filaments in vitro and to undergo liquid-liquid phase separation when mixed with poly-ubiquitin. Here, we determine the full-length cryo-EM structure of p62 and elucidate a structured double helical filament scaffold composed of the PB1-domain associated with the flexible C-terminal part and the solvent-accessible major groove. At different pH values and upon binding to soluble LC3, LC3-conjugated membranes and poly-ubiquitin, we observe p62 filament re-arrangements in the form of structural unwinding, disassembly, lateral association and bundling, respectively. In the cellular environment, under conditions of ATG5 knockdown leading to stalled autophagy, we imaged high-contrast layers consisting of p62 oligomers enwrapping lipid droplets by cryogenic electron tomography in situ, which we identified as calcium as well as phosphorus by compositional spectroscopy analysis. Together, we visualize the cellular ultrastructure of p62 oligomers with high calcium content as a potential early stage of autophagy.

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Authors
Berkamp, S., Jungbluth, L., Katranidis, A., Mostafavi, S., Korculanin, O., Lu, P.-H., Ickert, L., Dierig, M. M., Sharma, L., Thukral, L., Huesgen, P. F., Kononenko, N. L., Fitter, J., Dunin-Borkowski, R. E., & Sachse, C.
Affiliations
  • Forschungszentrum Jülich (DE)
  • Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (DE)
  • University of Freiburg (DE)
  • Institute of Genomics and Integrative Biology (IN)
  • University of Cologne (DE)
Corresponding author
  • Berkamp, Sabrina
  • Sachse, Carsten
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2025-11-28
Volume
16
Issue
1
Pages
10810-10810
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-025-66785-7
PMC
PMC12669770
OpenAlex
W4416780479
Cited by
12
References
6
Citations by year
2026: 9 · 2025: 2 · 2024: 1
FWCI
6.69
Type
journal article
Language
en
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  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
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  • FreiDok plus (Universitätsbibliothek Freiburg) (submittedVersion)
  • JuSER (Forschungszentrum Jülich) (submittedVersion, other-oa)
  • RWTH Publications (RWTH Aachen) (submittedVersion, other-oa)
  • RWTH Publications (RWTH Aachen)
Funders
  • Alexander von Humboldt-Stiftung
  • Wellcome Trust
  • Boehringer Ingelheim Fonds
  • Deutsche Forschungsgemeinschaft (411422114)
  • Forschungszentrum Jülich
  • HORIZON EUROPE European Research Council (101118656)
Topics
  • Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
Keywords
p62, selective autophagy receptors, PB1 domain, liquid-liquid phase separation, ATG5, autophagy, cryo-EM structure, cryo-electron tomography, cell ultrastructure
MeSH terms
Sequestosome-1 Protein, Autophagy, Calcium, HeLa Cells, Humans, Microtubule-Associated Proteins, Cryoelectron Microscopy, Lipid Droplets

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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