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- EMDB-52134: double helical p62/SQSTM1 filament -

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Basic information

Entry
Database: EMDB / ID: EMD-52134
Titledouble helical p62/SQSTM1 filament
Map data
Sample
  • Complex: p62/SQSTM1
    • Protein or peptide: Sequestosome-1
Keywordsautophagy / filaments / helical reconstruction / PROTEIN FIBRIL
Function / homology
Function and homology information


brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / intracellular membraneless organelle / aggrephagy / negative regulation of toll-like receptor 4 signaling pathway / amphisome / response to mitochondrial depolarisation / regulation of protein complex stability ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / intracellular membraneless organelle / aggrephagy / negative regulation of toll-like receptor 4 signaling pathway / amphisome / response to mitochondrial depolarisation / regulation of protein complex stability / autophagy of mitochondrion / endosome organization / pexophagy / aggresome / membraneless organelle assembly / regulation of mitochondrion organization / phagophore assembly site / ubiquitin-modified protein reader activity / Nuclear events mediated by NFE2L2 / regulation of canonical NF-kappaB signal transduction / cellular response to stress / endosomal transport / K63-linked polyubiquitin modification-dependent protein binding / Lewy body / temperature homeostasis / autolysosome / negative regulation of ferroptosis / molecular sequestering activity / energy homeostasis / mitophagy / immune system process / negative regulation of protein ubiquitination / protein catabolic process / response to ischemia / signaling adaptor activity / inclusion body / positive regulation of autophagy / ionotropic glutamate receptor binding / SH2 domain binding / autophagosome / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Pexophagy / protein kinase C binding / NRIF signals cell death from the nucleus / macroautophagy / positive regulation of long-term synaptic potentiation / positive regulation of protein localization to plasma membrane / sarcomere / PINK1-PRKN Mediated Mitophagy / ubiquitin binding / molecular condensate scaffold activity / protein sequestering activity / protein import into nucleus / P-body / receptor tyrosine kinase binding / PML body / autophagy / Interleukin-1 signaling / intracellular protein localization / sperm midpiece / Signaling by ALK fusions and activated point mutants / late endosome / KEAP1-NFE2L2 pathway / Neddylation / signaling receptor activity / ubiquitin-dependent protein catabolic process / cell differentiation / protein-macromolecule adaptor activity / intracellular signal transduction / positive regulation of apoptotic process / ubiquitin protein ligase binding / apoptotic process / protein kinase binding / protein-containing complex binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / nucleoplasm / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Ubiquitin associated domain ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Ubiquitin associated domain / Zinc finger ZZ-type signature. / Zinc finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsBerkamp S / Jungbluth L / Katranidis A / Mostafavi S / Sachse C
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101118656European Union
CitationJournal: Nat Commun / Year: 2025
Title: Structural organization of p62 filaments and the cellular ultrastructure of calcium-rich p62-enwrapped lipid droplet cargo.
Authors: Sabrina Berkamp / Lisa Jungbluth / Alexandros Katranidis / Siavash Mostafavi / Olivera Korculanin / Peng-Han Lu / Lotte Ickert / Maya M Dierig / Lokesh Sharma / Lipi Thukral / Pitter F ...Authors: Sabrina Berkamp / Lisa Jungbluth / Alexandros Katranidis / Siavash Mostafavi / Olivera Korculanin / Peng-Han Lu / Lotte Ickert / Maya M Dierig / Lokesh Sharma / Lipi Thukral / Pitter F Huesgen / Natalia L Kononenko / Jörg Fitter / Rafal E Dunin-Borkowski / Carsten Sachse /
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- ...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.
History
DepositionNov 19, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52134.png

Downloads & links

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Map

FileDownload / File: emd_52134.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.68 Å/pix.
x 300 pix.
= 503.34 Å		1.68 Å/pix.
x 300 pix.
= 503.34 Å		1.68 Å/pix.
x 300 pix.
= 503.34 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.8
Minimum - Maximum-7.571427 - 23.841529999999999
Average (Standard dev.)0.000000001127733 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 503.34003 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_52134_additional_1.map
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Half map: #1

Fileemd_52134_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52134_half_map_2.map
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Sample components

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Entire : p62/SQSTM1

EntireName: p62/SQSTM1
Components
  • Complex: p62/SQSTM1
    • Protein or peptide: Sequestosome-1

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Supramolecule #1: p62/SQSTM1

SupramoleculeName: p62/SQSTM1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sequestosome-1

MacromoleculeName: Sequestosome-1 / type: protein_or_peptide / ID: 1 / Number of copies: 40 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.55309 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
ASLTVKAYLL GKEDAAREIR RFSFCCSPEP EAEAEAAAGP GPCERLLSRV AALFPALRPG GFQAHYRDED GDLVAFSSDE ELTMAMSYV KDDIFRIYIK EKKEC

UniProtKB: Sequestosome-1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
300.0 mMNaClsodium chloride
2.5 mMMgSO4magnesium sulfate
10.0 uMZnCl2zinc chloride
0.5 mMC9H15O6PTCEP
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 4038 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 10.985 Å
Applied symmetry - Helical parameters - Δ&Phi: -26.141 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 600000
CTF correctionSoftware - Name: cryoSPARC (ver. 2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 1000000 / Software - Name: cryoSPARC (ver. 2)
Startup modelType of model: OTHER / Details: Featureless spheres
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0.7)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6tgy


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9hge:
PB1 domain of p62/SQSTM1

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