+Open data
-Basic information
Entry | Database: PDB / ID: 6cp2 | ||||||
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Title | SidC in complex with UbcH7~Ub | ||||||
Components |
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Keywords | LIGASE / Bacterial E3 Ligase / E2 / Ubiquitin | ||||||
Function / homology | Function and homology information cell cycle phase transition / ubiquitin-protein transferase activator activity / protein K11-linked ubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / cellular response to glucocorticoid stimulus / positive regulation of ubiquitin-protein transferase activity / female meiosis I / 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 / positive regulation of ubiquitin-protein transferase activity / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / fat pad development / cellular response to steroid hormone stimulus / female gonad development / seminiferous tubule development / male meiosis I / ubiquitin conjugating enzyme activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ubiquitin ligase complex / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / NF-kB is activated and signals survival / Regulation of PTEN localization / 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 / Gap-filling DNA repair synthesis and ligation in GG-NER / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / neuron projection morphogenesis / 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 / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling Similarity search - Function | ||||||
Biological species | Legionella pneumophila (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 | 6cp2.cif.gz | 306.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cp2.ent.gz | 251.1 KB | Display | PDB format |
PDBx/mmJSON format | 6cp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/6cp2 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/6cp2 | HTTPS FTP |
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-Related structure data
Related structure data | 6cp0C 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: 62243.879 Da / Num. of mol.: 1 / Mutation: C46A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RCR4 |
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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.) Homo sapiens (human) / Gene: UBE2L3, UBCE7, UBCH7 / Production host: Escherichia coli (E. coli) 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.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47 |
#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: 2.95 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: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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