+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8ikv | ||||||
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タイトル | pUbl depleted phospho-Parkin(K211N,R163D) in complex with pUb | ||||||
要素 |
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キーワード | LIGASE / E3 Ligase | ||||||
機能・相同性 | 機能・相同性情報 negative regulation of primary amine oxidase activity / positive regulation of retrograde transport, endosome to Golgi / regulation of lipid transport / positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / regulation of protein targeting to mitochondrion / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / negative regulation of glucokinase activity ...negative regulation of primary amine oxidase activity / positive regulation of retrograde transport, endosome to Golgi / regulation of lipid transport / positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / regulation of protein targeting to mitochondrion / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / negative regulation of glucokinase activity / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / Lewy body / protein K27-linked ubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of actin filament bundle assembly / positive regulation of mitochondrial fusion / free ubiquitin chain polymerization / protein K29-linked ubiquitination / regulation of synaptic vesicle transport / negative regulation of mitochondrial fusion / : / positive regulation of protein linear polyubiquitination / F-box domain binding / RBR-type E3 ubiquitin transferase / negative regulation by host of viral genome replication / cellular response to toxic substance / positive regulation of mitophagy / regulation of necroptotic process / regulation of cellular response to oxidative stress / regulation of dopamine metabolic process / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / dopaminergic synapse / positive regulation of dendrite extension / protein K6-linked ubiquitination / positive regulation of proteasomal protein catabolic process / norepinephrine metabolic process / protein localization to mitochondrion / positive regulation of protein localization to membrane / negative regulation of JNK cascade / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / cellular response to dopamine / mitochondrial fission / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / aggresome assembly / autophagy of mitochondrion / regulation of mitochondrion organization / regulation of canonical Wnt signaling pathway / aggresome / regulation of reactive oxygen species metabolic process / regulation of synaptic vesicle endocytosis / positive regulation of DNA binding / protein deubiquitination / positive regulation of mitochondrial fission / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / regulation of dopamine secretion / dopamine metabolic process / negative regulation of release of cytochrome c from mitochondria / startle response / protein monoubiquitination / Peptide chain elongation / cullin family protein binding / phospholipase binding / Selenocysteine synthesis / protein K63-linked ubiquitination / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / regulation of protein ubiquitination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / regulation of glucose metabolic process / mitophagy / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of reactive oxygen species metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / cellular response to unfolded protein / cellular response to manganese ion / protein autoubiquitination / proteasomal protein catabolic process / negative regulation of insulin secretion / protein K48-linked ubiquitination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ERAD pathway / ubiquitin ligase complex / cytosolic ribosome / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.35 Å | ||||||
データ登録者 | Lenka, D.R. / Kumar, A. | ||||||
資金援助 | インド, 1件
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引用 | ジャーナル: Elife / 年: 2024 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: ジャーナル: Elife / 年: 2024 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: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8ikv.cif.gz | 178.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8ikv.ent.gz | 134.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8ikv.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 8ikv_validation.pdf.gz | 6.6 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8ikv_full_validation.pdf.gz | 6.7 MB | 表示 | |
XML形式データ | 8ikv_validation.xml.gz | 35.8 KB | 表示 | |
CIF形式データ | 8ikv_validation.cif.gz | 47.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ik/8ikv ftp://data.pdbj.org/pub/pdb/validation_reports/ik/8ikv | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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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: 36510.609 Da / 分子数: 2 / 変異: R140P,R163D,K211N,Q347C / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PRKN, PARK2 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: O60260, RBR-type E3 ubiquitin transferase #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) Homo sapiens (ヒト) / 遺伝子: UBA52, UBCEP2 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P62987 #3: 化合物 | ChemComp-ZN / #4: 化合物 | #5: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.16 Å3/Da / 溶媒含有率: 43.16 % |
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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 詳細: 0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000 |
-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: シンクロトロン / サイト: ESRF / ビームライン: MASSIF-3 / 波長: 0.9677 Å |
検出器 | タイプ: DECTRIS EIGER X 4M / 検出器: PIXEL / 日付: 2022年7月22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: 0.9677 Å / 相対比: 1 |
反射 | 解像度: 2.35→38.39 Å / Num. obs: 31088 / % possible obs: 96.5 % / 冗長度: 3.1 % / CC1/2: 0.995 / Net I/σ(I): 7.7 |
反射 シェル | 解像度: 2.35→2.43 Å / Num. unique obs: 3040 / CC1/2: 0.686 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 5CAW 解像度: 2.35→38.242 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.048 / SU ML: 0.185 / 交差検証法: FREE R-VALUE / ESU R: 0.585 / ESU R Free: 0.243 / 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 | Biso mean: 44.93 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.35→38.242 Å
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拘束条件 |
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LS精密化 シェル |
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