+Open data
-Basic information
Entry | Database: PDB / ID: 3vtu | ||||||
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Title | Crystal structure of human LC3B_2-119 | ||||||
Components | Microtubule-associated proteins 1A/1B light chain 3B | ||||||
Keywords | PROTEIN BINDING / ubiquitin-like fold / Autophagy | ||||||
Function / homology | Function and homology information SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / Macroautophagy / Receptor Mediated Mitophagy / axoneme / autophagosome maturation ...SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / Macroautophagy / Receptor Mediated Mitophagy / axoneme / autophagosome maturation / autophagosome membrane / organelle membrane / mitophagy / autophagosome assembly / autophagosome / endomembrane system / PINK1-PRKN Mediated Mitophagy / Pexophagy / cellular response to starvation / mitochondrial membrane / macroautophagy / autophagy / KEAP1-NFE2L2 pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / microtubule / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Suzuki, H. / Kawasaki, M. / Kato, R. / Wakatsuki, S. | ||||||
Citation | Journal: Biochem.J. / Year: 2013 Title: Structural basis for phosphorylation-triggered autophagic clearance of Salmonella Authors: Rogov, V.V. / Suzuki, H. / Fiskin, E. / Wild, P. / Kniss, A. / Rozenknop, A. / Kato, R. / Kawasaki, M. / McEwan, D.G. / Lohr, F. / Guntert, P. / Dikic, I. / Wakatsuki, S. / Dotsch, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vtu.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vtu.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 3vtu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/3vtu ftp://data.pdbj.org/pub/pdb/validation_reports/vt/3vtu | HTTPS FTP |
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-Related structure data
Related structure data | 2lueC 3vtvC 3vtwC 3eciS C: citing same article (ref.) S: Starting model for refinement |
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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: 14479.567 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9GZQ8 | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 2.0M Ammonium sulfate, 0.1M Tri-sodium citrate, 0.2M Potassium sodium tartrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 18, 2010 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→22.91 Å / Num. obs: 15380 / % possible obs: 99 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.6→1.69 Å / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2184 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ECI Resolution: 1.6→22.91 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.744 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.106 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.097 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→22.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -12.5005 Å / Origin y: 2.4346 Å / Origin z: -3.5365 Å
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