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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 / 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)
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: 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. / Koronenko, N.L. / Fitter, J. ...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. / Koronenko, N.L. / Fitter, J. / Dunin-Borkowski, R.E. / Sachse, C.
History
DepositionNov 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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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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