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Open data
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Basic information
Entry | Database: PDB / ID: 5vo0 | ||||||
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Title | Structure of a TRAF6-Ubc13~Ub complex | ||||||
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![]() | TRANSFERASE | ||||||
Function / homology | ![]() p75NTR recruits signalling complexes / Interleukin-1 signaling / NOD1/2 Signaling Pathway / Ovarian tumor domain proteases / Ub-specific processing proteases / : / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination ...p75NTR recruits signalling complexes / Interleukin-1 signaling / NOD1/2 Signaling Pathway / Ovarian tumor domain proteases / Ub-specific processing proteases / : / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / tumor necrosis factor receptor binding / postreplication repair / hypothalamus gonadotrophin-releasing hormone neuron development / regulation of canonical NF-kappaB signal transduction / female meiosis I / positive regulation of protein monoubiquitination / positive regulation of intracellular signal transduction / positive regulation of double-strand break repair / mitochondrion transport along microtubule / fat pad development / non-canonical NF-kappaB signal transduction / E2 ubiquitin-conjugating enzyme / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / regulation of DNA repair / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / energy homeostasis / antiviral innate immune response / lipopolysaccharide-mediated signaling pathway / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / negative regulation of TORC1 signaling / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / tumor necrosis factor-mediated signaling pathway / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / positive regulation of DNA repair / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / lipid droplet / Downregulation of TGF-beta receptor signaling / neuron projection morphogenesis / 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 / 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 / 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 / TNFR1-induced NF-kappa-B signaling pathway Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Middleton, A.J. / Day, C.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The activity of TRAF RING homo- and heterodimers is regulated by zinc finger 1. Authors: Middleton, A.J. / Budhidarmo, R. / Das, A. / Zhu, J. / Foglizzo, M. / Mace, P.D. / Day, C.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157 KB | Display | ![]() |
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PDB format | ![]() | 123 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5vnzC ![]() 3hctS C: citing same article ( S: Starting model for refinement |
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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: 19765.547 Da / Num. of mol.: 2 / Fragment: residues 50-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q6IWL4*PLUS, RING-type E3 ubiquitin transferase #2: Protein | Mass: 17566.135 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P61088, E2 ubiquitin-conjugating enzyme #3: Protein | Mass: 8576.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-K / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.35 Å3/Da / Density % sol: 75.07 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100-200 mM Na/K tartrate, 11-15% PEG 3350 and 100 mM bis-Tris propane pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2016 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 3.9→128.4 Å / Num. obs: 14890 / % possible obs: 97.9 % / Redundancy: 4.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.091 / Rrim(I) all: 0.208 / Net I/σ(I): 7.9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HCT Resolution: 3.9→128.4 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.815 / SU B: 43.588 / SU ML: 0.592 / Cross valid method: THROUGHOUT / ESU R Free: 0.76 / 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: 110.268 Å2
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Refinement step | Cycle: 1 / Resolution: 3.9→128.4 Å
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