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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 / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / response to mitochondrial depolarisation / aggrephagy / Lewy body / negative regulation of toll-like receptor 4 signaling pathway / amphisome / regulation of protein complex stability ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / response to mitochondrial depolarisation / aggrephagy / Lewy body / negative regulation of toll-like receptor 4 signaling pathway / amphisome / regulation of protein complex stability / endosome organization / pexophagy / autophagy of mitochondrion / membraneless organelle assembly / phagophore assembly site / ubiquitin-modified protein reader activity / regulation of mitochondrion organization / regulation of canonical NF-kappaB signal transduction / Nuclear events mediated by NFE2L2 / aggresome / endosomal transport / K63-linked polyubiquitin modification-dependent protein binding / intracellular membraneless organelle / negative regulation of ferroptosis / temperature homeostasis / cellular response to stress / autolysosome / molecular sequestering activity / immune system process / mitophagy / energy homeostasis / sperm midpiece / signaling adaptor activity / inclusion body / ionotropic glutamate receptor binding / negative regulation of protein ubiquitination / positive regulation of autophagy / SH2 domain binding / p75NTR recruits signalling complexes / protein sequestering activity / autophagosome / NF-kB is activated and signals survival / Pexophagy / NRIF signals cell death from the nucleus / protein kinase C binding / sarcomere / ubiquitin binding / response to ischemia / positive regulation of long-term synaptic potentiation / PINK1-PRKN Mediated Mitophagy / positive regulation of protein localization to plasma membrane / macroautophagy / P-body / protein catabolic process / molecular condensate scaffold activity / receptor tyrosine kinase binding / PML body / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / intracellular protein localization / late endosome / signaling receptor activity / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / transcription by RNA polymerase II / cell differentiation / intracellular signal transduction / positive regulation of apoptotic process / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / protein-containing complex binding / glutamatergic synapse / enzyme binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / zinc ion binding / nucleoplasm / 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. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type 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: Berkamp S / Jungbluth L / Katranidis A / Mostafavi S / Korculanin O / Lu P-H / Ickert L / Dierig MM / Sharma L / Thukral L / Huesgen PF / Koronenko NL / Fitter J / Dunin-Borkowski RE / Sachse C
History
DepositionNov 19, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 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
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52134_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52134_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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