[English] 日本語
![](img/lk-miru.gif)
- PDB-3vtw: Crystal structure of T7-tagged Optineurin LIR-fused human LC3B_2-119 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3vtw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of T7-tagged Optineurin LIR-fused human LC3B_2-119 | ||||||
![]() | Optineurin, microtubule-associated proteins 1A/1B light chain 3B | ||||||
![]() | PROTEIN BINDING / ubiquitin-like fold / Autophagy | ||||||
Function / homology | ![]() SARS-CoV-2 modulates autophagy / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / ceramide binding / Golgi ribbon formation / negative regulation of receptor recycling / cell death / protein localization to Golgi apparatus / positive regulation of xenophagy / Golgi to plasma membrane protein transport / cellular response to nitrogen starvation ...SARS-CoV-2 modulates autophagy / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / ceramide binding / Golgi ribbon formation / negative regulation of receptor recycling / cell death / protein localization to Golgi apparatus / positive regulation of xenophagy / Golgi to plasma membrane protein transport / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / Macroautophagy / Receptor Mediated Mitophagy / Golgi organization / axoneme / organelle membrane / autophagosome membrane / mitophagy / autophagosome maturation / autophagosome assembly / autophagosome / polyubiquitin modification-dependent protein binding / cellular response to unfolded protein / endomembrane system / positive regulation of autophagy / negative regulation of canonical NF-kappaB signal transduction / PINK1-PRKN Mediated Mitophagy / Pexophagy / cellular response to starvation / TNFR1-induced NF-kappa-B signaling pathway / mitochondrial membrane / macroautophagy / Regulation of TNFR1 signaling / trans-Golgi network / autophagy / recycling endosome membrane / Regulation of PLK1 Activity at G2/M Transition / KEAP1-NFE2L2 pathway / protein-macromolecule adaptor activity / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / defense response to Gram-negative bacterium / microtubule / Golgi membrane / intracellular membrane-bounded organelle / innate immune response / ubiquitin protein ligase binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suzuki, H. / Kawasaki, M. / Kato, R. / Wakatsuki, S. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 168.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 134.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 470.3 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2lueC ![]() 3vtuSC ![]() 3vtvC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17175.408 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 170-181, RESIDUES 2-119 / Mutation: S170E, S171E, S173E, S174E, S177E Source method: isolated from a genetically manipulated source Details: The fusion protein of Optineurin LIR (RESIDUES 170-181) and Microtubule-associated proteins 1A/1B light chain 3B (RESIDUES 2-119) Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.84 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 2.0M Ammonium sulfate, 0.05M Tri-sodium citrate, 0.1M Potassium sodium tartrate, 5% Glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 5, 2011 |
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: 2.52→49.92 Å / Num. obs: 20055 / % possible obs: 97.5 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.52→2.66 Å / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 3 / Num. unique all: 2828 / % possible all: 95.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3VTU Resolution: 2.52→49.92 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.877 / SU B: 21.796 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 36.628 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.52→49.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.52→2.585 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|