+Open data
-Basic information
Entry | Database: PDB / ID: 3wap | ||||||
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Title | Crystal structure of Atg13 LIR-fused human LC3C_8-125 | ||||||
Components | Autophagy-related protein 13, Microtubule-associated proteins 1A/1B light chain 3C | ||||||
Keywords | PROTEIN TRANSPORT / UBIQUITIN-LIKE FOLD / AUTOPHAGY | ||||||
Function / homology | Function and homology information regulation of protein lipidation / Atg1/ULK1 kinase complex / protein exit from endoplasmic reticulum / response to mitochondrial depolarisation / aggrephagy / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / phosphatidylethanolamine binding ...regulation of protein lipidation / Atg1/ULK1 kinase complex / protein exit from endoplasmic reticulum / response to mitochondrial depolarisation / aggrephagy / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / phosphatidylethanolamine binding / protein kinase regulator activity / phagophore assembly site / positive regulation of protein targeting to mitochondrion / Macroautophagy / organelle membrane / autophagosome membrane / mitophagy / autophagosome maturation / autophagosome assembly / autophagosome / endomembrane system / positive regulation of autophagy / cellular response to starvation / protein serine/threonine kinase activator activity / macroautophagy / cytoplasmic ribonucleoprotein granule / cytoplasmic vesicle / microtubule / negative regulation of cell population proliferation / 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: 3.1 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 | 3wap.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wap.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 3wap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wap_validation.pdf.gz | 430.9 KB | Display | wwPDB validaton report |
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Full document | 3wap_full_validation.pdf.gz | 443.8 KB | Display | |
Data in XML | 3wap_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 3wap_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/3wap ftp://data.pdbj.org/pub/pdb/validation_reports/wa/3wap | HTTPS FTP |
-Related structure data
Related structure data | 3walC 3wamC 3wanC 3waoC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15401.719 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 436-447, 8-125 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 3C (RESIDUES 8-125) Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3C / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75143, UniProt: Q9BXW4 |
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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: 3.42 Å3/Da / Density % sol: 64.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Sodium acetate trihydrate, 8% PEG 4000, 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: 3.1→53.46 Å / Num. obs: 4045 / % possible obs: 98.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 3.1→3.27 Å / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 2.8 / Num. unique all: 588 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VTU Resolution: 3.1→53.46 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 54.548 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / 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: 144.718 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→53.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.181 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -16.4349 Å / Origin y: -19.2057 Å / Origin z: -13.3695 Å
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