+Open data
-Basic information
Entry | Database: PDB / ID: 5ypa | ||||||
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Title | p62/SQSTM1 ZZ domain with Lys-peptide | ||||||
Components | 78 kDa glucose-regulated protein,Sequestosome-1 | ||||||
Keywords | SIGNALING PROTEIN / Complex / p62/SQSTM1 / ZZ domain / Autophagy / N-end rule | ||||||
Function / homology | Function and homology information regulation of protein folding in endoplasmic reticulum / regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / cerebellum structural organization / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / : / maintenance of protein localization in endoplasmic reticulum ...regulation of protein folding in endoplasmic reticulum / regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / cerebellum structural organization / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / : / maintenance of protein localization in endoplasmic reticulum / cerebellar Purkinje cell layer development / protein targeting to vacuole involved in autophagy / negative regulation of IRE1-mediated unfolded protein response / IRE1alpha activates chaperones / regulation of Ras protein signal transduction / Lewy body / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / aggrephagy / response to mitochondrial depolarisation / amphisome / PERK regulates gene expression / protein folding in endoplasmic reticulum / pexophagy / endosome organization / regulation of protein complex stability / autophagy of mitochondrion / misfolded protein binding / post-translational protein targeting to membrane, translocation / phagophore assembly site / aggresome / regulation of mitochondrion organization / regulation of canonical NF-kappaB signal transduction / ERAD pathway / 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 / ER overload response / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / mitophagy / Signaling by ALK fusions and activated point mutants / endoplasmic reticulum-Golgi intermediate compartment / autophagosome / Regulation of HSF1-mediated heat shock response / cellular response to glucose starvation / negative regulation of protein-containing complex assembly / signaling adaptor activity / positive regulation of autophagy / energy homeostasis / : / protein folding chaperone / inclusion body / endoplasmic reticulum unfolded protein response / negative regulation of protein ubiquitination / sperm midpiece / ionotropic glutamate receptor binding / heat shock protein binding / p75NTR recruits signalling complexes / substantia nigra development / PINK1-PRKN Mediated Mitophagy / Pexophagy / cellular response to interleukin-4 / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / SH2 domain binding / response to endoplasmic reticulum stress / sarcomere / protein kinase C binding / ubiquitin binding / positive regulation of protein ubiquitination / positive regulation of long-term synaptic potentiation / response to ischemia / P-body / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / positive regulation of protein localization to plasma membrane / macroautophagy / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / 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 / melanosome / unfolded protein binding / protein-macromolecule adaptor activity / ribosome binding / late endosome / Platelet degranulation / signaling receptor activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å | ||||||
Authors | Kwon, D.H. / Kim, L. / Song, H.K. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Insights into degradation mechanism of N-end rule substrates by p62/SQSTM1 autophagy adapter. Authors: Kwon, D.H. / Park, O.H. / Kim, L. / Jung, Y.O. / Park, Y. / Jeong, H. / Hyun, J. / Kim, Y.K. / Song, H.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ypa.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ypa.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ypa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/5ypa ftp://data.pdbj.org/pub/pdb/validation_reports/yp/5ypa | HTTPS FTP |
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-Related structure data
Related structure data | 5yp7C 5yp8C 5ypbC 5ypcC 5ypeC 5ypfC 5ypgC 5yphC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6485.300 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA5, GRP78, SQSTM1, ORCA, OSIL / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P11021, UniProt: Q13501 #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Sequence details | LYS (-3 position) is synthetic residue generated by special enzyme | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.65 Å3/Da / Density % sol: 25.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, CaCl2, HEPES |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.2 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.502→21.993 Å / Num. obs: 2939 / % possible obs: 96.1 % / Redundancy: 4.5 % / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.5→2.54 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.502→21.993 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 16.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.502→21.993 Å
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Refine LS restraints |
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LS refinement shell |
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