9HGE | pdb_00009hge

PB1 domain of p62/SQSTM1

• PDB DOI: https://doi.org/10.2210/pdb9HGE/pdb
• EM Map EMD-52134: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-19 Released: 2025-12-03 
• Deposition Author(s): Berkamp, S., Jungbluth, L., Katranidis, A., Mostafavi, S., Sachse, C.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Starting Model: experimental

Literature

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

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.

(2025) Nat Commun 16: 10810-10810

• PubMed: 41315362 
• DOI: https://doi.org/10.1038/s41467-025-66785-7
• Primary Citation of Related Structures:  
  9HGE


• PubMed 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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Organizational Affiliation: 
• Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany. [e-mail].
Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany.
RWTH Aachen, I.Physikalisches Institut (IA), Aachen, Germany.
Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-1/Physics of Nanoscale Systems, Forschungszentrum Jülich, Jülich, Germany.
CECAD Excellence Center & Center for Physiology and Pathophysiology, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
Institute of Biology II, University of Freiburg, Schänzlestraße 1, Freiburg, Germany.
Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.
Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
CIBSS-Centre for Integrative Biological Signaling Studies, University of Freiburg, Schänzlestraße 1, Freiburg, Germany.
Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany.
Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany. [e-mail].
Department of Biology, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 40-mer - A40 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 462.12 kDa 
• Atom Count: 32,320 
• Modeled Residue Count: 4,160 
• Deposited Residue Count: 4,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sequestosome-1	A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, P, Q, R, S, T, U, V, W, X, Y, Z	104	Homo sapiens	Mutation(s): 0  Gene Names: SQSTM1, ORCA, OSIL
UniProt & NIH Common Fund Data Resources
Find proteins for Q13501 (Homo sapiens) Explore Q13501  Go to UniProtKB:  Q13501
PHAROS:  Q13501 GTEx:  ENSG00000161011

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Berkamp, S., Jungbluth, L., Katranidis, A., Mostafavi, S., Sachse, C.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101118656

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release
  
• Version 1.1: 2025-12-10
  Changes: Data collection, Database references