+Open data
-Basic information
Entry | Database: PDB / ID: 2zjd | ||||||
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Title | Crystal Structure of LC3-p62 complex | ||||||
Components |
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Keywords | Apoptosis inhibitor/Apoptosis / p62 / autophagy / LC3 / microtubule-associated protein 1 light chain 3 / Cytoplasm / Cytoplasmic vesicle / Lipoprotein / Membrane / Ubl conjugation pathway / Alternative splicing / Apoptosis / Differentiation / Endosome / Immune response / Metal-binding / Nucleus / Phosphoprotein / Zinc / Zinc-finger / Apoptosis inhibitor-Apoptosis COMPLEX | ||||||
Function / homology | Function and homology information Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / SARS-CoV-2 modulates autophagy / protein targeting to vacuole involved in autophagy / Lewy body / NF-kB is activated and signals survival ...Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / SARS-CoV-2 modulates autophagy / protein targeting to vacuole involved in autophagy / Lewy body / NF-kB is activated and signals survival / response to mitochondrial depolarisation / ceramide binding / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / Interleukin-1 signaling / KEAP1-NFE2L2 pathway / pexophagy / regulation of protein complex stability / endosome organization / non-membrane-bounded organelle assembly / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / aggresome / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / autolysosome / K63-linked polyubiquitin modification-dependent protein binding / intracellular non-membrane-bounded organelle / temperature homeostasis / Macroautophagy / immune system process / Receptor Mediated Mitophagy / axoneme / organelle membrane / autophagosome membrane / mitophagy / autophagosome maturation / autophagosome assembly / autophagosome / endomembrane system / positive regulation of autophagy / energy homeostasis / signaling adaptor activity / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / PINK1-PRKN Mediated Mitophagy / Pexophagy / cellular response to starvation / sarcomere / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / mitochondrial membrane / macroautophagy / protein kinase C binding / positive regulation of protein localization to plasma membrane / transcription coregulator activity / ionotropic glutamate receptor binding / P-body / protein catabolic process / PML body / autophagy / protein import into nucleus / KEAP1-NFE2L2 pathway / late endosome / protein-macromolecule adaptor activity / signaling receptor activity / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / microtubule / transcription by RNA polymerase II / cell differentiation / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||
Authors | Ichimura, Y. / Kumanomidou, T. / Sou, Y. / Mizushima, T. / Ezaki, J. / Ueno, T. / Kominami, E. / Yamane, T. / Tanaka, K. / Komatsu, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structural Basis for Sorting Mechanism of p62 in Selective Autophagy Authors: Ichimura, Y. / Kumanomidou, T. / Sou, Y.-S. / Mizushima, T. / Ezaki, J. / Ueno, T. / Kominami, E. / Yamane, T. / Tanaka, K. / Komatsu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zjd.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zjd.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 2zjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zjd_validation.pdf.gz | 453 KB | Display | wwPDB validaton report |
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Full document | 2zjd_full_validation.pdf.gz | 455.9 KB | Display | |
Data in XML | 2zjd_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 2zjd_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/2zjd ftp://data.pdbj.org/pub/pdb/validation_reports/zj/2zjd | HTTPS FTP |
-Related structure data
Related structure data | 1ugmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 15121.482 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9GZQ8 #2: Protein/peptide | Mass: 1190.156 Da / Num. of mol.: 2 Fragment: LC3 recognition sequence (LRS), UNP residue 334-344 Source method: obtained synthetically / Details: This sequence occurs naturally in mouse. / References: UniProt: Q64337 #3: Water | ChemComp-HOH / | |
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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: 2.15 Å3/Da / Density % sol: 42.87 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 23% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Nov 21, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→77.85 Å / Num. obs: 39943 / % possible obs: 98.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.31 / % possible all: 86 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UGM Resolution: 1.56→45.48 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.531 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.107 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→45.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.556→1.596 Å / Total num. of bins used: 20
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