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Open data
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Basic information
Entry | Database: PDB / ID: 5ms5 | ||||||
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Title | Low-salt structure of RavZ LIR2-fused human LC3B | ||||||
![]() | RavZ,Microtubule-associated proteins 1A/1B light chain 3B | ||||||
![]() | PROTEIN BINDING / Autophagy / Host-pathogen interaction / Protein binding /RavZ / LIR / LC3 | ||||||
Function / homology | ![]() host intracellular membrane-bounded organelle / symbiont-mediated suppression of host autophagy / SARS-CoV-2 modulates autophagy / protein delipidation / ceramide binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / phosphatidylinositol-3-phosphate binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs ...host intracellular membrane-bounded organelle / symbiont-mediated suppression of host autophagy / SARS-CoV-2 modulates autophagy / protein delipidation / ceramide binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / phosphatidylinositol-3-phosphate binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / Macroautophagy / Receptor Mediated Mitophagy / axoneme / organelle membrane / autophagosome membrane / mitophagy / autophagosome maturation / autophagosome assembly / autophagosome / endomembrane system / cysteine-type peptidase activity / PINK1-PRKN Mediated Mitophagy / Pexophagy / cellular response to starvation / mitochondrial membrane / macroautophagy / host cell cytoplasmic vesicle membrane / autophagy / KEAP1-NFE2L2 pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / microtubule / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / mitochondrion / proteolysis / extracellular region / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pantoom, S. / Vetter, I.R. / Wu, Y.W. | ||||||
![]() | ![]() Title: Elucidation of the anti-autophagy mechanism of the Legionella effector RavZ using semisynthetic LC3 proteins. Authors: Yang, A. / Pantoom, S. / Wu, Y.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.3 KB | Display | ![]() |
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PDB format | ![]() | 97 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460 KB | Display | ![]() |
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Full document | ![]() | 461.3 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ms2C ![]() 5ms6C ![]() 5ms7C ![]() 5ms8C ![]() 2z0eS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15968.087 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The fusion protein of RavZ LIR (RESIDUES 25-36) and Microtubule-associated proteins 1A/1B light chain 3B (RESIDUES 2-119) Source: (gene. exp.) ![]() ![]() ![]() Gene: lpg1683, MAP1LC3B, MAP1ALC3 / Plasmid: pMAL / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.69 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M citric acid anhydrous and 1.6 M ammonium sulfate PH range: 3.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2016 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99992 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→49.222 Å / Num. obs: 44250 / % possible obs: 100 % / Redundancy: 25.4 % / Biso Wilson estimate: 19.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1769 / Net I/σ(I): 14.69 |
Reflection shell | Resolution: 1.53→1.585 Å / Redundancy: 24.6 % / Rmerge(I) obs: 2.205 / Mean I/σ(I) obs: 1.42 / CC1/2: 0.165 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2Z0E Resolution: 1.53→49.222 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 28.35 / 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: 1.53→49.222 Å
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Refine LS restraints |
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LS refinement shell |
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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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