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Open data
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Basic information
Entry | Database: PDB / ID: 4uf9 | ||||||
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Title | Electron cryo-microscopy structure of PB1-p62 type T filaments | ||||||
![]() | SEQUESTOSOME-1 | ||||||
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Function / homology | ![]() protein localization to perinuclear region of cytoplasm / amphisome / selective autophagy / regulation of Ras protein signal transduction / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ciuffa, R. / Lamark, T. / Tarafder, A. / Guesdon, A. / Rybina, S. / Hagen, W.J.H. / Johansen, T. / Sachse, C. | ||||||
![]() | ![]() 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. | ||||||
Validation Report | ![]() ![]() ![]() | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmcif format | ![]() ![]() ![]() |
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PDB format | ![]() ![]() |
PDBML Plus | ![]() |
Others | ![]() |
-Related structure data
Related structure data | ![]() 2937CM ![]() 2936C ![]() 4uf8C C: citing same article ( M: map data used to model this data |
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Similar-shape strucutres |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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3 | ![]()
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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 °) |
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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.) ![]() ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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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![]() ![]() |
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, |
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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![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
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 |
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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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