: / : / protein modification process => GO:0036211 / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / IgG binding / mitochondrion transport along microtubule / fat pad development / female gonad development ...: / : / protein modification process => GO:0036211 / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / IgG binding / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / 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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / error-prone translesion synthesis / translesion synthesis / cytosolic ribosome / 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 / 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 / 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 Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain ...IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Roll / DNA/RNA polymerase superfamily / Alpha Beta Similarity search - Domain/homology
Polyubiquitin-B / Immunoglobulin G-binding protein G / Ubiquitin-60S ribosomal protein L40 / DNA polymerase iota Similarity search - Component
ImmunoglobulinG-bindingproteinG, DNApolymeraseiota / IgG-binding protein G / RAD30 homolog B / Eta2
Mass: 12348.556 Da / Num. of mol.: 1 / Fragment: UNP residues 304-357, 676-715 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sp., Homo sapiens / Gene: spg, POLI, RAD30B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P19909, UniProt: Q9UNA4, DNA-directed DNA polymerase
#2: Protein
Ubiquitin
Mass: 8859.106 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62988, UniProt: P0CG47*PLUS
Sequence details
ACCORDING TO THE AUTHORS THE N-TERMINAL PART IS A GB1 TAG USED FOR ENHANCEMENT OF PROTEIN ...ACCORDING TO THE AUTHORS THE N-TERMINAL PART IS A GB1 TAG USED FOR ENHANCEMENT OF PROTEIN SOLUBILITY. THEY CHOSE TO DEPOSIT ONLY THE C-TERMINAL PART OF THE SEQUENCE CORRESPONDING TO DNA POLYMERASE IOTA. THESE 2 SEGMENTS ARE LINKED BY THE RESIDUES GSDE
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Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR Details: Solution Structure of the human Polymerase iota UBM2-Ubiquitin Complex
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
2
1
2
3D HNCO
2
2
2
3D HNCA
2
3
2
3D HN(CA)CB
2
4
2
3DHN(CO)CA
2
5
2
3DHN(COCA)CB
3
6
3
3D (H)CCH-TOCSY
2
7
2
3D 1H-15N NOESY
3
8
3
3D 1H-13C NOESY
1
9
1
3D 1H-15N NOESY
4
10
4
3D 1H-13C NOESY
4
11
4
3D (H)CCH-TOCSY
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1 mM [U-100% 15N] entity_1-1, 4 mM entity_2-2, 90% H2O/10% D2O
90% H2O/10% D2O
2
3 mM [U-100% 15N] entity_1-3, 3 mM [U-100% 15N] entity_2-4, 90% H2O/10% D2O
90% H2O/10% D2O
3
3 mM [U-100% 13C; U-100% 15N] entity_1-5, 3 mM [U-100% 13C; U-100% 15N] entity_2-6, 100% D2O
100% D2O
4
1 mM [U-100% 13C; U-100% 15N] entity_1-7, 4 mM entity_2-8, 100% D2O
100% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
1mM
entity_1-1
[U-100% 15N]
1
4mM
entity_2-2
1
3mM
entity_1-3
[U-100% 15N]
2
3mM
entity_2-4
[U-100% 15N]
2
3mM
entity_1-5
[U-100% 13C; U-100% 15N]
3
3mM
entity_2-6
[U-100% 13C; U-100% 15N]
3
1mM
entity_1-7
[U-100% 13C; U-100% 15N]
4
4mM
entity_2-8
4
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
100
7
ambient
298K
2
100
7
ambient
298K
3
100
7
ambient
298K
4
100
7
ambient
298K
-
NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Varian INOVA
Varian
INOVA
800
1
Varian INOVA
Varian
INOVA
600
2
-
Processing
NMR software
Name
Version
Developer
Classification
X-PLOR NIH
2.19
Schwieters, Kuszewski, TjandraandClore
refinement
CYANA
Guntert, MumenthalerandWuthrich
structuresolution
Refinement
Method: simulated annealing / Software ordinal: 1
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 40 / Conformers submitted total number: 25
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