- PDB-2kwv: Solution Structure of UBM1 of murine Polymerase iota in Complex w... -
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基本情報
登録情報
データベース: PDB / ID: 2kwv
タイトル
Solution Structure of UBM1 of murine Polymerase iota in Complex with Ubiquitin
要素
DNA polymerase iota
Ubiquitin
キーワード
PROTEIN BINDING/SIGNALING PROTEIN / polymerase iota / ubiquitin / ubiquitin-binding motif / UBM / TLS / PROTEIN BINDING-SIGNALING PROTEIN complex
機能・相同性
機能・相同性情報
Translesion synthesis by POLI / Termination of translesion DNA synthesis / : / : / protein modification process => GO:0036211 / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development ...Translesion synthesis by POLI / Termination of translesion DNA synthesis / : / : / protein modification process => GO:0036211 / 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 / 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 / cellular response to UV-C / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / 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 類似検索 - 分子機能
DNA polymerase type-Y, HhH motif / IMS family HHH motif / 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. / Ribosomal L40e family / Ribosomal_L40e ...DNA polymerase type-Y, HhH motif / IMS family HHH motif / 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. / 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 類似検索 - ドメイン・相同性
Polyubiquitin-B / Ubiquitin-60S ribosomal protein L40 / DNA polymerase iota 類似検索 - 構成要素
1-2 mM [U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O
95% H2O/5% D2O
2
1-2 mM [U-95% 13C; U-99% 15N] DNA polymerase iota UBM1, 4-8 mM Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O
95% H2O/5% D2O
3
4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O
95% H2O/5% D2O
4
4-8 mM DNA polymerase iota UBM1, 1-2 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O
95% H2O/5% D2O
5
1.0 mM DNA polymerase iota UBM1, 4 mM [U-95% 13C; U-99% 15N] Ubiquitin, 25 mM sodium phosphate, 25 mM sodium chloride, 100 mM potassium chloride, 2 mM CHAPS, 0.15 mM PMSF, 0.2 % w/v sodium azide, 95% H2O/5% D2O
95% H2O/5% D2O
試料
濃度 (mg/ml)
単位
構成要素
Isotopic labeling
Conc. range (mg/ml)
Solution-ID
mM
DNA polymerase iota UBM1-1
[U-99% 15N]
1-2
1
mM
Ubiquitin-2
4-8
1
25mM
sodium phosphate-3
1
25mM
sodium chloride-4
1
100mM
potassium chloride-5
1
2mM
CHAPS-6
1
0.15mM
PMSF-7
1
0.2 %
sodium azide-8
1
mM
DNA polymerase iota UBM1-9
[U-95% 13C; U-99% 15N]
1-2
2
mM
Ubiquitin-10
4-8
2
25mM
sodium phosphate-11
2
25mM
sodium chloride-12
2
100mM
potassium chloride-13
2
2mM
CHAPS-14
2
0.15mM
PMSF-15
2
0.2 %
sodium azide-16
2
mM
DNA polymerase iota UBM1-17
4-8
3
mM
Ubiquitin-18
[U-99% 15N]
1-2
3
25mM
sodium phosphate-19
3
25mM
sodium chloride-20
3
100mM
potassium chloride-21
3
2mM
CHAPS-22
3
0.15mM
PMSF-23
3
0.2 %
sodium azide-24
3
mM
DNA polymerase iota UBM1-25
4-8
4
mM
Ubiquitin-26
[U-95% 13C; U-99% 15N]
1-2
4
25mM
sodium phosphate-27
4
25mM
sodium chloride-28
4
100mM
potassium chloride-29
4
2mM
CHAPS-30
4
0.15mM
PMSF-31
4
0.2 %
sodium azide-32
4
mM
DNA polymerase iota UBM1-33
1-2
5
mM
Ubiquitin-34
[U-95% 13C; U-99% 15N]
4-8
5
25mM
sodium phosphate-35
5
25mM
sodium chloride-36
5
100mM
potassium chloride-37
5
2mM
CHAPS-38
5
0.15mM
PMSF-39
5
0.2 %
sodium azide-40
5
試料状態
イオン強度: 0.189 / pH: 6.0 / 圧: ambient / 温度: 288 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
Bruker
AVANCE
600
1
Bruker Avance
Bruker
AVANCE
750
2
Bruker Avance
Bruker
AVANCE
900
3
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解析
NMR software
名称
バージョン
開発者
分類
Amber
9
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... andKollm
精密化
TopSpin
2.1
BrukerBiospin
collection
TopSpin
2.1
BrukerBiospin
解析
MOLMOL
2k.2
Koradi, BilleterandWuthrich
geometryoptimization
UNIO'08
1.0.4
T. Herrmann
peakpicking
UNIO'08
1.0.4
T. Herrmann
chemicalshiftassignment
UNIO'08
1.0.4
T. Herrmann
構造決定
DYANA
Guntert, BraunandWuthrich
構造決定
CARA
1.8.4
R. Keller
データ解析
CARA
1.8.4
R. Keller
chemicalshiftassignment
精密化
手法: molecular dynamics / ソフトェア番号: 1
NMR constraints
NOE constraints total: 2862 / NOE intraresidue total count: 684 / NOE long range total count: 630 / NOE medium range total count: 723 / NOE sequential total count: 825
代表構造
選択基準: lowest energy
NMRアンサンブル
コンフォーマー選択の基準: structures with the lowest energy 計算したコンフォーマーの数: 200 / 登録したコンフォーマーの数: 20