ISG15 transferase activity / ISG15-protein conjugation / : / : / protein modification process => GO:0036211 / E2 ubiquitin-conjugating enzyme / RSV-host interactions / Peptide chain elongation / ubiquitin conjugating enzyme activity / Selenocysteine synthesis ...ISG15 transferase activity / ISG15-protein conjugation / : / : / protein modification process => GO:0036211 / E2 ubiquitin-conjugating enzyme / RSV-host interactions / Peptide chain elongation / ubiquitin conjugating enzyme activity / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ubiquitin ligase complex / cytosolic ribosome / 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 / 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 / NOTCH3 Activation and Transmission of Signal to the Nucleus / 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 / 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 / Downregulation of TGF-beta receptor signaling / EGFR downregulation / 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 / 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 / Autodegradation of Cdh1 by Cdh1:APC/C / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / 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 / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 Similarity search - Function
Structures with the lowest energy in the lowest energy cluster
Representative
Model #1
closest to the mean structure
-
Components
#1: Protein
Ubiquitin/ISG15-conjugatingenzymeE2L6 / Ubiquitin-protein ligase L6 / Ubiquitin carrier protein L6 / UbcH8 / Retinoic acid-induced gene B ...Ubiquitin-protein ligase L6 / Ubiquitin carrier protein L6 / UbcH8 / Retinoic acid-induced gene B protein / RIG-B
Mass: 17659.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2L6, UBCH8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14933, ubiquitin-protein ligase
#2: Protein
Ubiquitin
Mass: 8622.922 Da / Num. of mol.: 1 / Mutation: G76C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A UBA80, UBCEP1, UBA52, UBB, UBC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P62988, UniProt: P0CG48*PLUS
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Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR Details: THESE MODELS WERE DETERMINED FROM DOCKING OF UBCH8 AND UBIQUITIN BASED ON CHEMICAL SHIFT PERTURBATION AND SATURATION TRANSFER EXPERIMENTS. AS THE STARTING STRUCTURES WERE X-RAY COORDINATES, ...Details: THESE MODELS WERE DETERMINED FROM DOCKING OF UBCH8 AND UBIQUITIN BASED ON CHEMICAL SHIFT PERTURBATION AND SATURATION TRANSFER EXPERIMENTS. AS THE STARTING STRUCTURES WERE X-RAY COORDINATES, NO SIDE CHAIN PROTONS ARE INCLUDED IN THE FINAL STRUCTURE FILE.
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 1H-15N HSQC
1
2
1
3D HN(CA)CB
1
3
1
3DCBCA(CO)NH
1
4
2
2D 1H-15N HSQC
1
5
2
3D HN(CA)CB
1
6
2
3DCBCA(CO)NH
1
7
3
2D 1H-15N HSQC with Cross Saturation
1
8
4
2D 1H-15N HSQC with Cross Saturation
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
0.35 mM [U-100% 13C; U-100% 15N] UbcH8-1, 0.35 mM Ubiquitin-2, 20 mM sodium phosphate-3, 1 mM EDTA-4, 250 mM sodium chloride-5, 50 mM Arginine-6, 50 mM Glutamic Acid-7, 90% H2O/10% D2O
90% H2O/10% D2O
2
0.35 mM UbcH8-8, 0.35 mM [U-100% 13C; U-100% 15N] Ubiquitin-9, 20 mM sodium phosphate-10, 1 mM EDTA-11, 250 mM sodium chloride-12, 50 mM Arginine-13, 50 mM Glutamic Acid-14, 90% H2O/10% D2O
90% H2O/10% D2O
3
0.35 mM [U-100% 15N; U-99% 2H] UbcH8-15, 0.35 mM Ubiquitin-16, 20 mM sodium phosphate-17, 1 mM EDTA-18, 250 mM sodium chloride-19, 50 mM Arginine-20, 50 mM Glutamic Acid-21, 90% H2O/10% D2O
90% H2O/10% D2O
4
0.35 mM UbcH8-22, 0.35 mM [U-100% 15N; U-99% 2H] Ubiquitin-23, 20 mM sodium phosphate-24, 1 mM EDTA-25, 250 mM sodium chloride-26, 50 mM Arginine-27, 50 mM Glutamic Acid-28, 90% H2O/10% D2O
Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 Details: Semi-rigid body docking using previously determined structures of UbcH8 and ubiquitin; calculated 1000 structures-200 low energy structures selected, Semi-flexible simulated annealing and ...Details: Semi-rigid body docking using previously determined structures of UbcH8 and ubiquitin; calculated 1000 structures-200 low energy structures selected, Semi-flexible simulated annealing and refinement with explicit water
NMR representative
Selection criteria: closest to the mean structure
NMR ensemble
Conformer selection criteria: Structures with the lowest energy in the lowest energy cluster Conformers calculated total number: 200 / Conformers submitted total number: 16
+
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