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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 5ohk | ||||||
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タイトル | Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (high resolution) | ||||||
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![]() | HYDROLASE / Deubiquitinase / DUB / Ubiquitin / USP | ||||||
機能・相同性 | ![]() protein K6-linked deubiquitination / protein K11-linked deubiquitination / pexophagy / autophagy of mitochondrion / deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / negative regulation of mitophagy / female meiosis I / peroxisomal membrane / positive regulation of protein monoubiquitination ...protein K6-linked deubiquitination / protein K11-linked deubiquitination / pexophagy / autophagy of mitochondrion / deubiquitinase activity / hypothalamus gonadotrophin-releasing hormone neuron development / negative regulation of mitophagy / female meiosis I / peroxisomal membrane / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / mitochondrial fusion / fat pad development / female gonad development / seminiferous tubule development / protein deubiquitination / 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 / 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 / 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 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Gersch, M. / Komander, D. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Mechanism and regulation of the Lys6-selective deubiquitinase USP30. 著者: Gersch, M. / Gladkova, C. / Schubert, A.F. / Michel, M.A. / Maslen, S. / Komander, D. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 92.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 66.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 968.7 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 973.9 KB | 表示 | |
XML形式データ | ![]() | 16.5 KB | 表示 | |
CIF形式データ | ![]() | 22.2 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 38469.422 Da / 分子数: 1 断片: UNP residues 64-178,UNP residues 217-357,UNP residues 432-502 変異: construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A),construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A),construct 13 (R179G, ...変異: construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A),construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A),construct 13 (R179G, Q180S, P181G, R182S, F348D, M350S, I353E, L358S, L359N, G360A) 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#2: タンパク質 | 分子量: 8558.857 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#3: 化合物 | ChemComp-ZN / |
#4: 化合物 | ChemComp-AYE / |
#5: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.46 Å3/Da / 溶媒含有率: 50 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.4 詳細: 10% (w/v) PEG 20000, 0.1 M sodium citrate pH 5.4, 0.2 M lithium sulfate |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2016年2月3日 |
放射 | モノクロメーター: Double Crystal, Si(111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.97949 Å / 相対比: 1 |
反射 | 解像度: 2.34→67.352 Å / Num. obs: 20131 / % possible obs: 99.18 % / 冗長度: 4.2 % / Biso Wilson estimate: 31.81 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.1701 / Rpim(I) all: 0.09162 / Net I/σ(I): 4.61 |
反射 シェル | 解像度: 2.34→2.424 Å / 冗長度: 4 % / Rmerge(I) obs: 0.7145 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 1978 / CC1/2: 0.848 / Rpim(I) all: 0.3804 / % possible all: 98.9 |
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解析
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精密化 | 構造決定の手法: ![]() 開始モデル: 2HD5 解像度: 2.34→67.352 Å / SU ML: 0.3 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 27.47
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.34→67.352 Å
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LS精密化 シェル |
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