+Open data
-Basic information
Entry | Database: PDB / ID: 6cp0 | ||||||
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Title | SdcA in complex with the E2, UbcH5C | ||||||
Components |
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Keywords | LIGASE / Complex / Bacterial E3 Ligase / E2 | ||||||
Function / homology | Function and homology information (E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / Signaling by BMP / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein monoubiquitination / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination ...(E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / Signaling by BMP / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein monoubiquitination / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / endosome membrane / DNA repair / apoptotic process / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Legionella pneumophila (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Wasilko, D.J. / Huang, Q. / Mao, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2018 Title: Insights into the ubiquitin transfer cascade catalyzed by theLegionellaeffector SidC. Authors: Wasilko, D.J. / Huang, Q. / Mao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cp0.cif.gz | 276.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cp0.ent.gz | 225.1 KB | Display | PDB format |
PDBx/mmJSON format | 6cp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/6cp0 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/6cp0 | HTTPS FTP |
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-Related structure data
Related structure data | 6cp2C 4trgS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 62006.695 Da / Num. of mol.: 1 / Mutation: C45A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RCR3 |
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#2: Protein | Mass: 16874.305 Da / Num. of mol.: 1 / Mutation: C85S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D3, UBC5C, UBCH5C / Production host: Escherichia coli (E. coli) References: UniProt: P61077, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme |
#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: 3.72 Å3/Da / Density % sol: 66.94 % / Description: Small, plate-like crystals |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5 M ammonium sulfate, 3% glycerol, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6309 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6309 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 25193 / % possible obs: 96.4 % / Redundancy: 4 % / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.9→2.95 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TRG Resolution: 3.01→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.892 / SU B: 42.876 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R Free: 0.408 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.161 Å2
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Refinement step | Cycle: 1 / Resolution: 3.01→50 Å
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Refine LS restraints |
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