- PDB-5ujn: Representative 2-conformer ensembles of K27-linked Ub2 from RDC data -
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基本情報
登録情報
データベース: PDB / ID: 5ujn
タイトル
Representative 2-conformer ensembles of K27-linked Ub2 from RDC data
要素
Ubiquitin
キーワード
SIGNALING PROTEIN / diubiquitin / K27 / polyubiquitin chain
機能・相同性
機能・相同性情報
hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / 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 / energy homeostasis ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / 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 / 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 / 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 類似検索 - 分子機能
150 uM [U-99% 15N] distal K27-Ub2, 20 mM NaPhosphate, 0.02 % NaN3, 95% H2O/5% D2O
15N-labelled K27-Ub2 with the distal Ub 15N, and proximal Ub 14N. pH 6.8 20 mM NaPhosphate, 0.02% NaN3
Distal K27-Ub2
95% H2O/5% D2O
solution
2
150 uM [U-99% 15N] proximal K27-Ub2, 20 mM NaPhosphate, 0.02 % NaN3, 95% H2O/5% D2O
15N-labelled K27-Ub2 with the distal Ub 14N, and proximal Ub 15N. pH 6.8 20 mM NaPhosphate, 0.02% NaN3
Proximal K27-Ub2
95% H2O/5% D2O
試料
濃度 (mg/ml)
構成要素
Isotopic labeling
Solution-ID
150uM
distal K27-Ub2
[U-99% 15N]
1
20mM
NaPhosphate
naturalabundance
1
0.02 %
NaN3
naturalabundance
1
150uM
proximal K27-Ub2
[U-99% 15N]
2
20mM
NaPhosphate
naturalabundance
2
0.02 %
NaN3
naturalabundance
2
試料状態
詳細: pH 6.8 20 mM NaPhospahte / イオン強度: 20 mM / Label: conditions_1 / pH: 6.8 / 圧: 1 atm / 温度: 296 K
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NMR測定
NMRスペクトロメーター
タイプ
製造業者
モデル
磁場強度 (MHz)
Spectrometer-ID
Bruker AVANCE III
Bruker
AVANCEIII
600
1
Bruker AVANCE III
Bruker
AVANCEIII
800
2
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解析
NMR software
名称
開発者
分類
ARMOR
BerlinK, Castaneda, CA, FushmanD
精密化
Sparky
Goddard
chemicalshiftassignment
Sparky
Goddard
peakpicking
精密化
手法: na / ソフトェア番号: 1 詳細: Using ~100 RDC restraints, ARMOR was used to select 2-member ensembles of K27-Ub2 that are in best agreement with RDC data. This generated a total of 10 2-conformer ensembles for this entry.
代表構造
選択基準: structures with best agreement with rdc data
NMRアンサンブル
コンフォーマー選択の基準: structures with the best agreement with RDC data 計算したコンフォーマーの数: 100000 / 登録したコンフォーマーの数: 20