+Open data
-Basic information
Entry | Database: PDB / ID: 3wan | ||||||
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Title | Crystal structure of Atg13 LIR-fused human LC3A_2-121 | ||||||
Components | Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3A | ||||||
Keywords | PROTEIN BINDING / UBIQUITIN-LIKE FOLD / AUTOPHAGY | ||||||
Function / homology | Function and homology information regulation of protein lipidation / cellular response to oxygen-glucose deprivation / Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / autophagy of mitochondrion / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / SMAD protein signal transduction ...regulation of protein lipidation / cellular response to oxygen-glucose deprivation / Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / autophagy of mitochondrion / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / SMAD protein signal transduction / phosphatidylethanolamine binding / protein kinase regulator activity / phagophore assembly site / response to iron(II) ion / positive regulation of protein targeting to mitochondrion / autolysosome / Macroautophagy / Receptor Mediated Mitophagy / p38MAPK cascade / organelle membrane / autophagosome membrane / mitophagy / autophagosome maturation / autophagosome assembly / autophagosome / positive regulation of autophagy / JNK cascade / cellular response to copper ion / PINK1-PRKN Mediated Mitophagy / cellular response to amino acid starvation / cellular response to starvation / protein serine/threonine kinase activator activity / macroautophagy / response to lead ion / phospholipid binding / cellular response to hydrogen peroxide / late endosome / microtubule binding / microtubule / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / glutamatergic synapse / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein kinase binding / mitochondrion / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Suzuki, H. / Tabata, K. / Morita, E. / Kawasaki, M. / Kato, R. / Dobson, R.C.J. / Yoshimori, T. / Wakatsuki, S. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism. Authors: Suzuki, H. / Tabata, K. / Morita, E. / Kawasaki, M. / Kato, R. / Dobson, R.C. / Yoshimori, T. / Wakatsuki, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wan.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wan.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 3wan.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wan_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
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Full document | 3wan_full_validation.pdf.gz | 454 KB | Display | |
Data in XML | 3wan_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 3wan_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/3wan ftp://data.pdbj.org/pub/pdb/validation_reports/wa/3wan | HTTPS FTP |
-Related structure data
Related structure data | 3walC 3wamC 3waoC 3wapC 3vtuS S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 15755.913 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 436-447, 2-121 Source method: isolated from a genetically manipulated source Details: THE FUSION PROTEIN OF AUTOPHAGY-RELATED GENE 13 LIR (RESIDUES 436-447), LINKER (GLY SER) AND MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3A (RESIDUES 2-121) Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3A / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75143, UniProt: Q9H492 #2: Chemical | ChemComp-MPD / ( | #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: 2.03 Å3/Da / Density % sol: 39.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 12% MPD, 0.1M Sodium chloride, 0.1M Sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→47.88 Å / Num. obs: 24414 / % possible obs: 99 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.77→1.87 Å / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 4.9 / Num. unique all: 3447 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VTU Resolution: 1.77→47.88 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.514 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 18.692 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→47.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.773→1.819 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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