+Open data
-Basic information
Entry | Database: PDB / ID: 4q5e | ||||||
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Title | Shigella Effector Kinase OspG bound to E2-Ub UbcH7-Ub Conjugate | ||||||
Components |
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Keywords | UNKNOWN FUNCTION / PROTEIN BINDING / protein-protein complex / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / kinase fold / inhibition of NF-kB pathway | ||||||
Function / homology | Function and homology information Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / Pexophagy / Interleukin-1 signaling / Aggrephagy / Regulation of pyruvate metabolism / Peroxisomal protein import ...Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / Pexophagy / Interleukin-1 signaling / Aggrephagy / Regulation of pyruvate metabolism / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Transferases; Transferring phosphorus-containing groups / cell cycle phase transition / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / ubiquitin-protein transferase activator activity / E3 ubiquitin ligases ubiquitinate target proteins / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / 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 Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Formation of TC-NER Pre-Incision Complex / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / Ub-specific processing proteases / 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 / modification-dependent protein catabolic process / protein polyubiquitination / protein tag activity / ubiquitin-protein transferase activity / host cell / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / peroxisome / presynapse / kinase activity / ubiquitin-dependent protein catabolic process / transcription coactivator activity / protein autophosphorylation / cell population proliferation / protein ubiquitination / ubiquitin protein ligase binding / regulation of DNA-templated transcription / enzyme binding / RNA binding / extracellular space / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Shigella sonnei Ss046 (bacteria) Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.869 Å | ||||||
Authors | Cygler, M. / Grishin, A.M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: Structure / Year: 2014 Title: Structural Basis for the Inhibition of Host Protein Ubiquitination by Shigella Effector Kinase OspG. Authors: Grishin, A.M. / Condos, T.E. / Barber, K.R. / Campbell-Valois, F.X. / Parsot, C. / Shaw, G.S. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q5e.cif.gz | 184.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q5e.ent.gz | 152.5 KB | Display | PDB format |
PDBx/mmJSON format | 4q5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q5e_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
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Full document | 4q5e_full_validation.pdf.gz | 436.9 KB | Display | |
Data in XML | 4q5e_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 4q5e_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/4q5e ftp://data.pdbj.org/pub/pdb/validation_reports/q5/4q5e | HTTPS FTP |
-Related 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: 20116.547 Da / Num. of mol.: 1 / Fragment: unp residues 26-193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella sonnei Ss046 (bacteria) / Strain: 2457T / Gene: ospG, SSON_P170 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star References: UniProt: Q3YTH2, Transferases; Transferring phosphorus-containing groups |
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#2: Protein | Mass: 8642.873 Da / Num. of mol.: 1 / Mutation: C17S, C137S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SCD2, UBE2L3, UBI4, YLL039C / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG63, ubiquitin-protein ligase |
#3: Protein | Mass: 18052.662 Da / Num. of mol.: 1 / Mutation: K48R, G76C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBCE7, UBCH7, UBE2L3, UBI4 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P68036, ubiquitin-protein ligase |
#4: 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: 2.6 Å3/Da / Density % sol: 52.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100mM Hepes 8.2, 15% PEG 4000, 100 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77.2 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 13, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: dcm WITH CRYO-COOLED 1ST CRYSTAL SAGITALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.87→50 Å / Num. obs: 40758 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 36.84 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 54.98
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.869→44.758 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 24.4 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.869→44.758 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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