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- PDB-9hge: PB1 domain of p62/SQSTM1 -

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Basic information

Entry
Database: PDB / ID: 9hge
TitlePB1 domain of p62/SQSTM1
ComponentsSequestosome-1
KeywordsPROTEIN FIBRIL / autophagy / filaments / helical reconstruction
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 / aggrephagy / response to mitochondrial depolarisation / 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 / aggrephagy / response to mitochondrial depolarisation / Lewy body / negative regulation of toll-like receptor 4 signaling pathway / amphisome / regulation of protein complex stability / endosome organization / autophagy of mitochondrion / pexophagy / 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 / inclusion body / ionotropic glutamate receptor binding / signaling adaptor activity / positive regulation of autophagy / negative regulation of protein ubiquitination / protein sequestering activity / SH2 domain binding / autophagosome / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Pexophagy / NRIF signals cell death from the nucleus / protein kinase C binding / ubiquitin binding / sarcomere / positive regulation of long-term synaptic potentiation / response to ischemia / PINK1-PRKN Mediated Mitophagy / positive regulation of protein localization to plasma membrane / macroautophagy / P-body / protein catabolic process / molecular condensate scaffold activity / PML body / receptor tyrosine kinase binding / autophagy / Interleukin-1 signaling / protein import into nucleus / Signaling by ALK fusions and activated point mutants / KEAP1-NFE2L2 pathway / 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 / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsBerkamp, S. / Jungbluth, L. / Katranidis, A. / Mostafavi, S. / Sachse, C.
Funding supportEuropean Union, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sequestosome-1
B: Sequestosome-1
C: Sequestosome-1
D: Sequestosome-1
E: Sequestosome-1
F: Sequestosome-1
G: Sequestosome-1
H: Sequestosome-1
I: Sequestosome-1
J: Sequestosome-1
K: Sequestosome-1
L: Sequestosome-1
M: Sequestosome-1
N: Sequestosome-1
O: Sequestosome-1
P: Sequestosome-1
Q: Sequestosome-1
R: Sequestosome-1
S: Sequestosome-1
T: Sequestosome-1
U: Sequestosome-1
V: Sequestosome-1
W: Sequestosome-1
X: Sequestosome-1
Y: Sequestosome-1
Z: Sequestosome-1
a: Sequestosome-1
b: Sequestosome-1
c: Sequestosome-1
d: Sequestosome-1
e: Sequestosome-1
f: Sequestosome-1
g: Sequestosome-1
h: Sequestosome-1
i: Sequestosome-1
j: Sequestosome-1
k: Sequestosome-1
l: Sequestosome-1
m: Sequestosome-1
n: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)462,12440
Polymers462,12440
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Sequestosome-1 / EBI3-associated protein of 60 kDa / EBIAP / p60 / Phosphotyrosine-independent ligand for the Lck ...EBI3-associated protein of 60 kDa / EBIAP / p60 / Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa / Ubiquitin-binding protein p62


Mass: 11553.090 Da / Num. of mol.: 40
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1, ORCA, OSIL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13501
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: p62/SQSTM1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 DE3
Buffer solutionpH: 6
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
2300 mMsodium chlorideNaCl1
32.5 mMmagnesium sulfateMgSO41
410 uMzinc chlorideZnCl21
50.5 mMTCEPC9H15O6P1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 100000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4038
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC2particle selection
2SerialEMimage acquisition
4cryoSPARC2CTF correction
7UCSF ChimeraX1.8model fitting
9RELION3.0.7initial Euler assignment
10RELION3.0.7final Euler assignment
11cryoSPARC3.0.7classification
12cryoSPARC23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -26.141 ° / Axial rise/subunit: 10.985 Å / Axial symmetry: D1
Particle selectionNum. of particles selected: 1000000
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 600000 / Symmetry type: HELICAL
Atomic model buildingPDB-ID: 6tgy

6tgy


Accession code: 6tgy / Source name: PDB / Type: experimental model

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