+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2936 | |||||||||
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Title | Electron cryo-microscopy structure of PB1-p62 filaments | |||||||||
Map data | 3D reconstruction of PB1(1-102) p62 | |||||||||
Sample |
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Keywords | Selective autophagy / autophagy receptor / autophagy scaffold / p62/SQSTM1 / single-particle helical reconstruction | |||||||||
Function / homology | Function and homology information brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / response to stress / protein binding / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / Lewy body / aggrephagy / response to mitochondrial depolarisation / positive regulation of mitophagy in response to mitochondrial depolarization ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / response to stress / protein binding / protein targeting to vacuole involved in autophagy / regulation of Ras protein signal transduction / Lewy body / aggrephagy / response to mitochondrial depolarisation / positive regulation of mitophagy in response to mitochondrial depolarization / amphisome / negative regulation of toll-like receptor 4 signaling pathway / non-membrane-bounded organelle assembly / regulation of autophagy of mitochondrion / pexophagy / endosome organization / regulation of protein complex stability / protein heterooligomerization / autophagy of mitochondrion / molecular sequestering activity / 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 / intracellular non-membrane-bounded organelle / neurotrophin TRK receptor signaling pathway / mitophagy / positive regulation of macroautophagy / 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 / molecular condensate scaffold activity / NF-kB is activated and signals survival / SH2 domain binding / sarcomere / protein sequestering activity / protein kinase C binding / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / P-body / apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / macroautophagy / protein catabolic process / protein localization / PML body / receptor tyrosine kinase binding / autophagy / 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 / cytoplasmic vesicle / transcription by RNA polymerase II / cell differentiation / lysosome / endosome / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / protein phosphorylation / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 10.9 Å | |||||||||
Authors | Ciuffa R / Lamark T / Tarafder A / Guesdon A / Rybina S / Hagen WJH / Johansen T / Sachse C | |||||||||
Citation | Journal: Cell Rep / Year: 2015 Title: The selective autophagy receptor p62 forms a flexible filamentous helical scaffold. Authors: Rodolfo Ciuffa / Trond Lamark / Abul K Tarafder / Audrey Guesdon / Sofia Rybina / Wim J H Hagen / Terje Johansen / Carsten Sachse / Abstract: The scaffold protein p62/SQSTM1 is involved in protein turnover and signaling and is commonly found in dense protein bodies in eukaryotic cells. In autophagy, p62 acts as a selective autophagy ...The scaffold protein p62/SQSTM1 is involved in protein turnover and signaling and is commonly found in dense protein bodies in eukaryotic cells. In autophagy, p62 acts as a selective autophagy receptor that recognizes and shuttles ubiquitinated proteins to the autophagosome for degradation. The structural organization of p62 in cellular bodies and the interplay of these assemblies with ubiquitin and the autophagic marker LC3 remain to be elucidated. Here, we present a cryo-EM structural analysis of p62. Together with structures of assemblies from the PB1 domain, we show that p62 is organized in flexible polymers with the PB1 domain constituting a helical scaffold. Filamentous p62 is capable of binding LC3 and addition of long ubiquitin chains induces disassembly and shortening of filaments. These studies explain how p62 assemblies provide a large molecular scaffold for the nascent autophagosome and reveal how they can bind ubiquitinated cargo. | |||||||||
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_2936.map.gz | 2.4 MB | EMDB map data format | |
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Header (meta data) | emd-2936-v30.xml emd-2936.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
Images | emd_2936.png | 438.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2936 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2936 | HTTPS FTP |
-Related structure data
Related structure data | 4uf8MC 2937C 4uf9C M: atomic model generated by this map C: citing same article (ref.) |
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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_2936.map.gz / Format: CCP4 / Size: 4.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D reconstruction of PB1(1-102) p62 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : PB1(1-102) domain of p62/Sqstm1
Entire | Name: PB1(1-102) domain of p62/Sqstm1 |
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Components |
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-Supramolecule #1000: PB1(1-102) domain of p62/Sqstm1
Supramolecule | Name: PB1(1-102) domain of p62/Sqstm1 / type: sample / ID: 1000 / Details: Helical polymer / Oligomeric state: Helical / Number unique components: 1 |
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Molecular weight | Experimental: 11.3 KDa / Theoretical: 11.3 KDa / Method: Theoretical weight of construct |
-Macromolecule #1: Sequestosome-1
Macromolecule | Name: Sequestosome-1 / type: protein_or_peptide / ID: 1 / Name.synonym: p62/SQSTM1 / Oligomeric state: Helical / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 11.3 KDa / Theoretical: 11.3 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: pOPTM-p62-PB1_K103STOP_E104STOP |
Sequence | UniProtKB: Sequestosome-1 GO: phagophore assembly site, autophagy of mitochondrion, P-body, P-body, positive regulation of protein phosphorylation, immune system process, protein serine/threonine kinase activity, protein ...GO: phagophore assembly site, autophagy of mitochondrion, P-body, P-body, positive regulation of protein phosphorylation, immune system process, protein serine/threonine kinase activity, protein kinase C binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, nucleus, nucleus, nucleoplasm, cytoplasm, cytoplasm, cytoplasm, lysosome, lysosome, endosome, late endosome, autophagosome, autophagosome, autophagosome, endoplasmic reticulum, endoplasmic reticulum, cytosol, cytosol, cytosol, cytosol, cytosol, cytosol, cytosol, cytosol, cytosol, cytosol, protein phosphorylation, ubiquitin-dependent protein catabolic process, autophagy, autophagy, autophagy, apoptotic process, response to stress, protein localization, zinc ion binding, regulation of mitochondrion organization, endosomal transport, inclusion body, aggresome, aggresome, macroautophagy, positive regulation of macroautophagy, PML body, protein kinase binding, cell differentiation, receptor tyrosine kinase binding, cytoplasmic vesicle, intracellular signal transduction, SH2 domain binding, identical protein binding, identical protein binding, identical protein binding, identical protein binding, identical protein binding, protein homodimerization activity, positive regulation of apoptotic process, negative regulation of apoptotic process, regulation of canonical NF-kappaB signal transduction, ubiquitin binding, positive regulation of transcription by RNA polymerase II, regulation of Ras protein signal transduction, metal ion binding, neurotrophin TRK receptor signaling pathway, neurotrophin TRK receptor signaling pathway, protein heterooligomerization, extracellular exosome, K63-linked polyubiquitin modification-dependent protein binding, apoptotic signaling pathway, positive regulation of mitophagy in response to mitochondrial depolarization, regulation of autophagy of mitochondrion InterPro: PB1 domain, UBA-like superfamily, Ubiquitin-associated domain, Zinc finger, ZZ-type |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 0.25 mg/mL |
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Buffer | pH: 7.5 / Details: 50 mM Tris pH 7.5, 100 mM NaCl, DTT 4 mM |
Grid | Details: glow-discharged C-flat 1.2/1.3 and 200 mesh Quantifoil multi-A grids |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER / Method: Backside blotting |
-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 / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Date | Feb 21, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 994 / Average electron dose: 15 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: CTFFIND, convolution images, Wiener filter reconstruction |
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Final angle assignment | Details: SPIDER |
Final reconstruction | Applied symmetry - Helical parameters - Δz: 12.99 Å Applied symmetry - Helical parameters - Δ&Phi: 30.77 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.9 Å / Resolution method: OTHER / Software - Name: SPRING |
Details | All of the image processing was carried using the SPRING package. |