(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / sperm flagellum / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) ...(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / sperm flagellum / protein autoubiquitination / protein K48-linked ubiquitination / 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 / 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 / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / 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 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Termination of translesion DNA synthesis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Stabilization of p53 / EGFR downregulation Similarity search - Function
Mass: 16650.068 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-147 / Mutation: YES Source method: isolated from a genetically manipulated source Details: K85 SIDE CHAIN IS COVALENTLY LINKED TO G76 IN CHAIN B. Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62837, ubiquitin-protein ligase
#2: Protein
POLYUBIQUITIN-C / UBIQUITIN
Mass: 8922.141 Da / Num. of mol.: 2 / Fragment: RESIDUES 77-152 Source method: isolated from a genetically manipulated source Details: G76 IN CHAIN B IS COVALENTLY LINKED TO K85 SIDE CHAIN IN CHAIN A. Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG48
#3: Protein
E3UBIQUITIN-PROTEINLIGASERNF38 / RING FINGER PROTEIN 38 / RNF38
Mass: 9135.328 Da / Num. of mol.: 1 / Fragment: RESIDUES 439-515 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H0F5, ubiquitin-protein ligase
Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
-
Details
Sequence details
N-TERMINAL METHIONINE IS CLEAVED DURING PURIFICATION. CYS85 IS MUTATED TO LYSINE. CONTAINS N- ...N-TERMINAL METHIONINE IS CLEAVED DURING PURIFICATION. CYS85 IS MUTATED TO LYSINE. CONTAINS N-TERMINAL GSGGS DUE TO CLONING CONTAIN N-TERMINAL GS DUE TO CLONING
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.5 Å3/Da / Density % sol: 50.72 % / Description: NONE
Crystal grow
Details: 50 MM HEPES, PH 7.5, 0.2 M MAGNESIUM ACETATE AND 13% (W/V) PEG 8K
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97949 Å / Relative weight: 1
Reflection
Resolution: 1.53→63.7 Å / Num. obs: 66991 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Biso Wilson estimate: 20.99 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.1
Reflection shell
Resolution: 1.53→1.57 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.6 / % possible all: 99.8
-
Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
SCALA
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→63.687 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 18.26 / Stereochemistry target values: ML Details: IN CHAIN C, RESIDUES 389-393 AND 463-C ARE DISORDERED. IN CHAIN D, RESIDUES 72-76 ARE DISORDERED. RESIDUES WITH POOR SIDE CHAIN ELECTRON DENSITY WERE BUILT AS ALANINE.
Rfactor
Num. reflection
% reflection
Rfree
0.1926
3391
5.1 %
Rwork
0.1828
-
-
obs
0.1833
66991
99.78 %
Solvent computation
Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.894 Å2 / ksol: 0.328 e/Å3