+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2937 | |||||||||
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Title | Electron cryo-microscopy structure of PB1-p62 type T filaments | |||||||||
Map data | 3D reconstruction of PB1(1-122) type T | |||||||||
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 / protein binding / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / positive regulation of mitophagy in response to mitochondrial depolarization ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein binding / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / positive regulation of mitophagy in response to mitochondrial depolarization / negative regulation of toll-like receptor 4 signaling pathway / regulation of autophagy of mitochondrion / autophagy of mitochondrion / pexophagy / protein heterooligomerization / regulation of protein complex stability / endosome organization / response to stress / non-membrane-bounded organelle assembly / molecular sequestering activity / ubiquitin-modified protein reader activity / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / Nuclear events mediated by NFE2L2 / negative regulation of ferroptosis / autolysosome / endosomal transport / intracellular non-membrane-bounded organelle / temperature homeostasis / immune system process / K63-linked polyubiquitin modification-dependent protein binding / neurotrophin TRK receptor signaling pathway / positive regulation of macroautophagy / mitophagy / autophagosome / positive regulation of autophagy / signaling adaptor activity / energy homeostasis / inclusion body / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / ionotropic glutamate receptor binding / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / Pexophagy / sarcomere / positive regulation of protein localization to plasma membrane / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / macroautophagy / apoptotic signaling pathway / protein kinase C binding / P-body / protein catabolic process / PML body / receptor tyrosine kinase binding / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / protein localization / Signaling by ALK fusions and activated point mutants / late endosome / signaling receptor activity / Neddylation / protein-macromolecule adaptor activity / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / endosome / cell differentiation / lysosome / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / protein phosphorylation / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein-containing complex binding / protein kinase binding / apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / mitochondrion / zinc ion binding / extracellular exosome / nucleoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 10.3 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_2937.map.gz | 12.2 MB | EMDB map data format | |
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Header (meta data) | emd-2937-v30.xml emd-2937.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
Images | emd_2937.png | 443 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2937 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2937 | HTTPS FTP |
-Validation report
Summary document | emd_2937_validation.pdf.gz | 213.4 KB | Display | EMDB validaton report |
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Full document | emd_2937_full_validation.pdf.gz | 212.5 KB | Display | |
Data in XML | emd_2937_validation.xml.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2937 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2937 | HTTPS FTP |
-Related structure data
Related structure data | 4uf9MC 2936C 4uf8C 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_2937.map.gz / Format: CCP4 / Size: 18.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D reconstruction of PB1(1-122) type T | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.372 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(1-122) domain of p62/Sqstm1
Entire | Name: PB1(1-122) domain of p62/Sqstm1 |
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Components |
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-Supramolecule #1000: PB1(1-122) domain of p62/Sqstm1
Supramolecule | Name: PB1(1-122) 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: 13.7 KDa / Theoretical: 13.7 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: 13.7 KDa / Theoretical: 13.7 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant plasmid: pOPTM-p62-PB1 |
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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Date | Oct 9, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 443 / Average electron dose: 10 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | All of the image processing was carried using the SPRING package. |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 10.09 Å Applied symmetry - Helical parameters - Δ&Phi: 26.71 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.3 Å / Resolution method: OTHER / Software - Name: SPRING |
CTF correction | Details: CTFFIND, convolution images, Wiener filter reconstruction |
Final angle assignment | Details: SPIDER |