+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 / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / autophagy of mitochondrion ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / autophagy of mitochondrion / pexophagy / regulation of protein complex stability / endosome organization / 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 / 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 / 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 / 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 / ubiquitin protein ligase binding / 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 / mitochondrion / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol 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 | 62.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uf9.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 4uf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uf9_validation.pdf.gz | 718.7 KB | Display | wwPDB validaton report |
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Full document | 4uf9_full_validation.pdf.gz | 723.2 KB | Display | |
Data in XML | 4uf9_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 4uf9_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/4uf9 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/4uf9 | HTTPS FTP |
-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 FIELD / 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 Accession code: 2KKC / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 10.3 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 10.3 Å
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