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Open data
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Basic information
Entry | Database: PDB / ID: 6cp2 | ||||||
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Title | SidC in complex with UbcH7~Ub | ||||||
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![]() | LIGASE / Bacterial E3 Ligase / E2 / Ubiquitin | ||||||
Function / homology | ![]() cell cycle phase transition / ubiquitin-protein transferase activator activity / protein K11-linked ubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / cellular response to glucocorticoid stimulus / female meiosis I / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / positive regulation of protein targeting to mitochondrion ...cell cycle phase transition / ubiquitin-protein transferase activator activity / protein K11-linked ubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / cellular response to glucocorticoid stimulus / female meiosis I / positive regulation of ubiquitin-protein transferase activity / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / positive regulation of protein targeting to mitochondrion / fat pad development / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ubiquitin conjugating enzyme activity / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / neuron projection morphogenesis / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wasilko, D.J. / Huang, Q. / Mao, Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 306.6 KB | Display | ![]() |
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PDB format | ![]() | 251.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.7 KB | Display | ![]() |
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Full document | ![]() | 466.8 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 38.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6cp0C ![]() 4trgS 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
#1: Protein | Mass: 62243.879 Da / Num. of mol.: 1 / Mutation: C46A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 17915.625 Da / Num. of mol.: 1 / Mutation: C86K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P68036, E2 ubiquitin-conjugating enzyme |
#3: Protein | Mass: 8720.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.29 % / Description: Hexagonal rods |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 16% PEG 3000, 0.1 M Tris pH 9.0 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 24890 / % possible obs: 99.9 % / Redundancy: 13.8 % / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 2.9→2.95 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4TRG Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.875 / SU B: 38.969 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.854 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→50 Å
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Refine LS restraints |
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