+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10502 | ||||||||||||
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Title | Cryo-EM structure of p62-PB1 filament (S-type) | ||||||||||||
Map data | Globally sharpened map | ||||||||||||
Sample |
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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 / Lewy body / aggrephagy / response to mitochondrial depolarisation / amphisome / pexophagy ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / : / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / Lewy body / aggrephagy / response to mitochondrial depolarisation / amphisome / pexophagy / endosome organization / regulation of protein complex stability / autophagy of mitochondrion / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / K63-linked polyubiquitin modification-dependent protein binding / Nuclear events mediated by NFE2L2 / autolysosome / temperature homeostasis / endosomal transport / immune system process / mitophagy / Signaling by ALK fusions and activated point mutants / autophagosome / signaling adaptor activity / positive regulation of autophagy / energy homeostasis / inclusion body / negative regulation of protein ubiquitination / sperm midpiece / ionotropic glutamate receptor binding / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / Pexophagy / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / SH2 domain binding / sarcomere / protein kinase C binding / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / P-body / positive regulation of protein localization to plasma membrane / macroautophagy / protein catabolic process / protein localization / PML body / receptor tyrosine kinase binding / autophagy / cellular response to reactive oxygen species / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / protein-macromolecule adaptor activity / late endosome / signaling receptor activity / Neddylation / ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / cell differentiation / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / 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 | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||
Authors | Huber ST / Jakobi AJ / Mortensen SA / Sachse C | ||||||||||||
Funding support | Germany, 3 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis of p62/SQSTM1 helical filaments and their role in cellular cargo uptake. Authors: Arjen J Jakobi / Stefan T Huber / Simon A Mortensen / Sebastian W Schultz / Anthimi Palara / Tanja Kuhm / Birendra Kumar Shrestha / Trond Lamark / Wim J H Hagen / Matthias Wilmanns / Terje ...Authors: Arjen J Jakobi / Stefan T Huber / Simon A Mortensen / Sebastian W Schultz / Anthimi Palara / Tanja Kuhm / Birendra Kumar Shrestha / Trond Lamark / Wim J H Hagen / Matthias Wilmanns / Terje Johansen / Andreas Brech / Carsten Sachse / Abstract: p62/SQSTM1 is an autophagy receptor and signaling adaptor with an N-terminal PB1 domain that forms the scaffold of phase-separated p62 bodies in the cell. The molecular determinants that govern PB1 ...p62/SQSTM1 is an autophagy receptor and signaling adaptor with an N-terminal PB1 domain that forms the scaffold of phase-separated p62 bodies in the cell. The molecular determinants that govern PB1 domain filament formation in vitro remain to be determined and the role of p62 filaments inside the cell is currently unclear. We here determine four high-resolution cryo-EM structures of different human and Arabidopsis PB1 domain assemblies and observed a filamentous ultrastructure of p62/SQSTM1 bodies using correlative cellular EM. We show that oligomerization or polymerization, driven by a double arginine finger in the PB1 domain, is a general requirement for lysosomal targeting of p62. Furthermore, the filamentous assembly state of p62 is required for autophagosomal processing of the p62-specific cargo KEAP1. Our results show that using such mechanisms, p62 filaments can be critical for cargo uptake in autophagy and are an integral part of phase-separated p62 bodies. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10502.map.gz | 22.2 MB | EMDB map data format | |
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Header (meta data) | emd-10502-v30.xml emd-10502.xml | 18.9 KB 18.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10502_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_10502.png | 157.1 KB | ||
Masks | emd_10502_msk_1.map | 64 MB | Mask map | |
Others | emd_10502_additional.map.gz emd_10502_half_map_1.map.gz emd_10502_half_map_2.map.gz | 22.1 MB 49.6 MB 49.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10502 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10502 | HTTPS FTP |
-Related structure data
Related structure data | 6th3MC 6tgnC 6tgpC 6tgsC 6tgyC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10502.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Globally sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10502_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered map
File | emd_10502_additional.map | ||||||||||||
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Annotation | Unfiltered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map #1
File | emd_10502_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half map #1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map #2
File | emd_10502_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map #2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : p62-PB1 domain filament (L-type)
Entire | Name: p62-PB1 domain filament (L-type) |
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Components |
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-Supramolecule #1: p62-PB1 domain filament (L-type)
Supramolecule | Name: p62-PB1 domain filament (L-type) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #1: Sequestosome-1
Macromolecule | Name: Sequestosome-1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.704609 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MASLTVKAYL LGKEDAAREI RRFSFCCSPE PEAEAEAAAG PGPCERLLSR VAALFPALRP GGFQAHYRDE DGDLVAFSSD EELTMAMSY VKDDIFRIYI KEKKECRRDH RPPCAQEAPR NMV |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 / Details: 50 mM TRIS (pH 7.5), 100 mM NaCl, 4 mM DTT |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2277 / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |