+Open data
-Basic information
Entry | Database: PDB / ID: 4uf9 | ||||||
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Title | Electron cryo-microscopy structure of PB1-p62 type T filaments | ||||||
Components | SEQUESTOSOME-1 | ||||||
Keywords | SIGNALING PROTEIN / 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 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 | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 10.3 Å | ||||||
Authors | Ciuffa, R. / Lamark, T. / Tarafder, A. / Guesdon, A. / Rybina, S. / Hagen, W.J.H. / 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4uf9.cif.gz | 58.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uf9.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 4uf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/4uf9 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/4uf9 | HTTPS FTP |
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-Related structure data
Related structure data | 2937MC 2936C 4uf8C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 20 / Rise per n subunits: 10.09 Å / Rotation per n subunits: -26.71 °) |
-Components
#1: Protein | Mass: 13704.609 Da / Num. of mol.: 3 / Fragment: PB1 DOMAIN, RESIDUES 1-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPTM-P62-PB1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q13501 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: PB1(1-122) DOMAIN OF P62- SQSTM-1 / Type: COMPLEX |
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Buffer solution | Name: 50 MM TRIS PH 7.5, 100 MM NACL, DTT 4 MM / pH: 7.5 / Details: 50 MM TRIS PH 7.5, 100 MM NACL, DTT 4 MM |
Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 77, INSTRUMENT- HOMEMADE PLUNGER, METHOD- BACKSIDE BLOTTING, |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Oct 9, 2012 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Image recording | Electron dose: 10 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 443 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: CTFFIND, CONVOLUTION IMAGES, WIENER FILTER RECONSTRUCTION | ||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 10.3 Å / Num. of particles: 182238 / Nominal pixel size: 1.372 Å / Actual pixel size: 1.372 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2937. (DEPOSITION ID: 13204). Symmetry type: HELICAL | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--NMR | ||||||||||||
Atomic model building | PDB-ID: 2KKC | ||||||||||||
Refinement | Highest resolution: 10.3 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 10.3 Å
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