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Yorodumi- PDB-4wz3: Crystal structure of the complex between LubX/LegU2/Lpp2887 U-box... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wz3 | |||||||||
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Title | Crystal structure of the complex between LubX/LegU2/Lpp2887 U-box 1 and Homo sapiens UBE2D2 | |||||||||
Components |
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Keywords | LIGASE / alpha/beta protein / effector / activating enzyme / structural genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG | |||||||||
Function / homology | Function and homology information (E3-independent) E2 ubiquitin-conjugating enzyme / cellular response to misfolded protein / E2 ubiquitin-conjugating enzyme / protein quality control for misfolded or incompletely synthesized proteins / ubiquitin conjugating enzyme activity / positive regulation of proteolysis / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes ...(E3-independent) E2 ubiquitin-conjugating enzyme / cellular response to misfolded protein / E2 ubiquitin-conjugating enzyme / protein quality control for misfolded or incompletely synthesized proteins / ubiquitin conjugating enzyme activity / positive regulation of proteolysis / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / CLEC7A (Dectin-1) signaling / Z disc / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / host cell / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / protein-folding chaperone binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Legionella pneumophila (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Stogios, P.J. / Quaile, A.T. / Skarina, T. / Nocek, B. / Di Leo, R. / Yim, V. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | |||||||||
Funding support | United States, 2items
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Citation | Journal: Structure / Year: 2015 Title: Molecular Characterization of LubX: Functional Divergence of the U-Box Fold by Legionella pneumophila. Authors: Quaile, A.T. / Urbanus, M.L. / Stogios, P.J. / Nocek, B. / Skarina, T. / Ensminger, A.W. / Savchenko, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wz3.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wz3.ent.gz | 118.3 KB | Display | PDB format |
PDBx/mmJSON format | 4wz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wz3_validation.pdf.gz | 429.7 KB | Display | wwPDB validaton report |
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Full document | 4wz3_full_validation.pdf.gz | 432.6 KB | Display | |
Data in XML | 4wz3_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 4wz3_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/4wz3 ftp://data.pdbj.org/pub/pdb/validation_reports/wz/4wz3 | HTTPS FTP |
-Related structure data
Related structure data | 4wz0SC 4wz2C 4xi1C 4ddiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16796.213 Da / Num. of mol.: 1 / Mutation: C85S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62837, ubiquitin-protein ligase |
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#2: Protein | Mass: 24818.092 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Paris / Gene: lubX, lpp2887 / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5X159, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 15 mg/ml of E2D2.(C85S)-Ub conjugate and an equimolar concentration of LubX (1-186), 0.2 M sodium tartrate, 0.1 M Tris-Cl (pH 8.5) and 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789897 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789897 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. obs: 11243 / % possible obs: 99 % / Redundancy: 5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.05 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 5 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 4.07 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DDI, LubX U-box 1 WT PDB code 4WZ0 Resolution: 2.7→35.855 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.03 / 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: 2.7→35.855 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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