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- PDB-3sy2: Crystal structure of the Salmonella E3 ubiquitin ligase SopA in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3sy2 | ||||||
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Title | Crystal structure of the Salmonella E3 ubiquitin ligase SopA in complex with the human E2 UbcH7 | ||||||
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![]() | LIGASE/SIGNALING PROTEIN / pentapeptide / HECT domain / HECT E3 / HECT E3 ubiquitin ligase / E2 ubiquitin conjugating enzyme / ubiquitin / protein-protein complex / effector protein / ubiquitin transfer / ubiquitination / LIGASE-SIGNALING PROTEIN complex | ||||||
Function / homology | ![]() cell cycle phase transition / ubiquitin-protein transferase activator activity / HECT-type E3 ubiquitin transferase / protein K11-linked ubiquitination / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / cellular response to steroid hormone stimulus / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity ...cell cycle phase transition / ubiquitin-protein transferase activator activity / HECT-type E3 ubiquitin transferase / protein K11-linked ubiquitination / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein targeting to mitochondrion / cellular response to steroid hormone stimulus / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of protein ubiquitination / Regulation of TNFR1 signaling / protein modification process / Regulation of necroptotic cell death / protein polyubiquitination / ubiquitin-protein transferase activity / host cell / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / presynapse / ubiquitin-dependent protein catabolic process / cell population proliferation / transcription coactivator activity / protein ubiquitination / ubiquitin protein ligase binding / regulation of DNA-templated transcription / enzyme binding / RNA binding / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Diao, J. / Lin, D.Y. / Chen, J. | ||||||
![]() | ![]() Title: Crystal structures of two bacterial HECT-like E3 ligases in complex with a human E2 reveal atomic details of pathogen-host interactions. Authors: Lin, D.Y. / Diao, J. / Chen, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 585.9 KB | Display | ![]() |
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PDB format | ![]() | 485.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3sqvC ![]() 1c4zS ![]() 2qyuS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 69235.219 Da / Num. of mol.: 2 Fragment: C-terminal beta-helix domain and HECT-like domain (UNP residues 165-782) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: sopA, STM2066 / Plasmid: pMCSG7 / Production host: ![]() ![]() References: UniProt: Q8ZNR3, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein | Mass: 18033.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES, 1.6 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 26, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03324 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 31621 / Num. obs: 31621 / % possible obs: 86.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 85.18 Å2 / Rsym value: 0.147 / Net I/σ(I): 7.19 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.39 / Num. unique all: 3105 / Rsym value: 0.52 / % possible all: 83.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2QYU AND 1C4Z Resolution: 3.27→45.424 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 27.69 / 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 / Bsol: 55.369 Å2 / ksol: 0.307 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.27→45.424 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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