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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: 8ik6 | ||||||
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タイトル | pUbl depleted Parkin complex with pUbiquitin | ||||||
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![]() | LIGASE / E3 Ligase | ||||||
機能・相同性 | ![]() : / positive regulation of retrograde transport, endosome to Golgi / regulation of lipid transport / positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / regulation of protein targeting to mitochondrion / cellular response to L-glutamine ...: / positive regulation of retrograde transport, endosome to Golgi / regulation of lipid transport / positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / regulation of protein targeting to mitochondrion / cellular response to L-glutamine / negative regulation of exosomal secretion / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / response to curcumin / cellular response to hydrogen sulfide / protein K27-linked ubiquitination / negative regulation of mitochondrial fusion / Parkin-FBXW7-Cul1 ubiquitin ligase complex / protein K29-linked ubiquitination / free ubiquitin chain polymerization / Lewy body / positive regulation of protein linear polyubiquitination / negative regulation of actin filament bundle assembly / host-mediated suppression of viral genome replication / positive regulation of mitophagy / RBR-type E3 ubiquitin transferase / regulation of synaptic vesicle transport / F-box domain binding / positive regulation of mitochondrial fusion / regulation of cellular response to oxidative stress / regulation of necroptotic process / mitochondrial fragmentation involved in apoptotic process / mitochondrion localization / regulation of dopamine metabolic process / positive regulation of dendrite extension / negative regulation of excitatory postsynaptic potential / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K6-linked ubiquitination / dopaminergic synapse / norepinephrine metabolic process / autophagy of mitochondrion / positive regulation of type 2 mitophagy / protein localization to mitochondrion / cellular response to L-glutamate / response to insecticide / positive regulation of proteasomal protein catabolic process / cellular response to dopamine / positive regulation of protein localization to membrane / cellular response to toxic substance / mitochondrial fission / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / aggresome assembly / protein K11-linked ubiquitination / negative regulation of synaptic transmission, glutamatergic / regulation of mitochondrion organization / ubiquitin conjugating enzyme binding / regulation of canonical Wnt signaling pathway / positive regulation of mitochondrial membrane potential / negative regulation of JNK cascade / aggresome / regulation of reactive oxygen species metabolic process / response to corticosterone / positive regulation of mitochondrial fission / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / response to muscle activity / negative regulation of release of cytochrome c from mitochondria / regulation of dopamine secretion / startle response / dopamine metabolic process / positive regulation of ATP biosynthetic process / cullin family protein binding / negative regulation of reactive oxygen species metabolic process / Peptide chain elongation / regulation of glucose metabolic process / 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 / protein K63-linked ubiquitination / protein deubiquitination / Viral mRNA Translation / regulation of synaptic vesicle endocytosis / regulation of protein ubiquitination / Maturation of protein E / protein monoubiquitination / Maturation of protein E / cellular response to manganese ion / negative regulation of mitochondrial fission / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / cellular response to unfolded protein / GTP hydrolysis and joining of the 60S ribosomal subunit / ER Quality Control Compartment (ERQC) / ubiquitin ligase complex / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Lenka, D.R. / Kumar, A. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans. 著者: Lenka, D.R. / Dahe, S.V. / Antico, O. / Sahoo, P. / Prescott, A.R. / Muqit, M.M.K. / Kumar, A. #1: ![]() タイトル: Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans 著者: Lenka, D. / Dahe, S. / Antico, O. / Sahoo, P. / Prescott, A.R. / Muqit, M.M.K. / Kumar, A. | ||||||
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 | ![]() | 160.8 KB | 表示 | ![]() |
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PDB形式 | ![]() | 120.7 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 | ![]() | 5.3 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 5.4 MB | 表示 | |
XML形式データ | ![]() | 29.5 KB | 表示 | |
CIF形式データ | ![]() | 38.3 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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2 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 36802.086 Da / 分子数: 2 / 変異: R140P,Q347C,A383N,S384L,G385Y,T386F,T387Q,T388S / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 8599.758 Da / 分子数: 2 / 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-SO4 / #5: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | Has protein modification | Y | |
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-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: 3.98 Å3/Da / 溶媒含有率: 69.07 % |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 詳細: 1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2022年10月29日 |
放射 | 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: 0.8856 Å / 相対比: 1 |
反射 | 解像度: 3.3→39.15 Å / Num. obs: 20948 / % possible obs: 92.85 % / 冗長度: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1928 / Net I/σ(I): 8.4 |
反射 シェル | 解像度: 3.3→3.56 Å / Num. unique obs: 4366 / CC1/2: 0.5 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: 5N2W 解像度: 3.3→39.15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 31.9 / SU ML: 0.457 / 交差検証法: FREE R-VALUE / ESU R Free: 0.491 / 詳細: Hydrogens have been added in their riding positions
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ |
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精密化ステップ | サイクル: LAST / 解像度: 3.3→39.15 Å
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拘束条件 |
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LS精密化 シェル |
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