+Open data
-Basic information
Entry | Database: PDB / ID: 5lxh | ||||||
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Title | GABARAP-L1 ATG4B LIR Complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / LIR / GABARAP / ATG8 / LC3 | ||||||
Function / homology | Function and homology information otolith mineralization completed early in development / protein-phosphatidylethanolamide deconjugating activity / protein delipidation / microautophagy / glycophagy / aggrephagy / Tat protein binding / GABA receptor binding / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus ...otolith mineralization completed early in development / protein-phosphatidylethanolamide deconjugating activity / protein delipidation / microautophagy / glycophagy / aggrephagy / Tat protein binding / GABA receptor binding / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phosphatidylethanolamine binding / autophagy of mitochondrion / cellular response to nitrogen starvation / Macroautophagy / beta-tubulin binding / autophagosome membrane / autophagosome maturation / autophagosome assembly / mitophagy / cysteine-type peptidase activity / autophagosome / macroautophagy / cytoplasmic vesicle membrane / phospholipid binding / protein processing / autophagy / protein transport / cytoplasmic vesicle / scaffold protein binding / endopeptidase activity / microtubule / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / ubiquitin protein ligase binding / Golgi apparatus / endoplasmic reticulum / mitochondrion / proteolysis / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Mouilleron, S. / Skytte Rasmussen, M. / Kumar Shrestha, B. / Wirth, M. / Bowitz Larsen, K. / Abudu Princely, Y. / Sjottem, E. / Tooze, S. / Lamark, T. / Johansen, T. / Lee, R. | ||||||
Citation | Journal: Autophagy / Year: 2017 Title: ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8. Authors: Skytte Rasmussen, M. / Mouilleron, S. / Kumar Shrestha, B. / Wirth, M. / Lee, R. / Bowitz Larsen, K. / Abudu Princely, Y. / O'Reilly, N. / Sjttem, E. / Tooze, S.A. / Lamark, T. / Johansen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lxh.cif.gz | 177.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lxh.ent.gz | 142.3 KB | Display | PDB format |
PDBx/mmJSON format | 5lxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lxh_validation.pdf.gz | 494 KB | Display | wwPDB validaton report |
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Full document | 5lxh_full_validation.pdf.gz | 499 KB | Display | |
Data in XML | 5lxh_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 5lxh_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/5lxh ftp://data.pdbj.org/pub/pdb/validation_reports/lx/5lxh | HTTPS FTP |
-Related structure data
Related structure data | 5lxiC 2r2qS 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 14598.667 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta, pLysS / References: UniProt: Q9H0R8 #2: Protein/peptide | Mass: 1209.257 Da / Num. of mol.: 3 / Fragment: UNP residues 384-393 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q9Y4P1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 2.24 Å3/Da / Density % sol: 45.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.968 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→51 Å / Num. obs: 55946 / % possible obs: 100 % / Redundancy: 5.1 % / CC1/2: 0.99 / Rsym value: 0.05 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.58→1.6 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.6 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2R2Q Resolution: 1.58→48.822 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→48.822 Å
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Refine LS restraints |
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LS refinement shell |
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