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基本情報
登録情報 | データベース: PDB / ID: 4bm9 | ||||||
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タイトル | Structure of the autoinhibited Parkin catalytic domain | ||||||
![]() | E3 UBIQUITIN-PROTEIN LIGASE PARKIN | ||||||
![]() | LIGASE / NEURODEGENERATIVE DISEASE | ||||||
機能・相同性 | ![]() 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 / negative regulation of spontaneous neurotransmitter secretion / regulation of protein targeting to mitochondrion / 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 / negative regulation of spontaneous neurotransmitter secretion / regulation of protein targeting to mitochondrion / negative regulation of intralumenal vesicle formation / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / negative regulation of exosomal secretion / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / Lewy body / protein K27-linked ubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / positive regulation of mitochondrial fusion / regulation of synaptic vesicle transport / negative regulation of actin filament bundle assembly / free ubiquitin chain polymerization / protein K29-linked ubiquitination / negative regulation of mitochondrial fusion / positive regulation of mitophagy in response to mitochondrial depolarization / 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 / autophagy of mitochondrion / regulation of dopamine metabolic process / dopaminergic synapse / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of dendrite extension / protein K6-linked ubiquitination / norepinephrine metabolic process / positive regulation of proteasomal protein catabolic 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 / cellular response to dopamine / positive regulation of tumor necrosis factor-mediated signaling pathway / mitochondrial fission / protein K11-linked ubiquitination / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / regulation of canonical Wnt signaling pathway / aggresome / regulation of reactive oxygen species metabolic process / regulation of synaptic vesicle endocytosis / dopamine uptake involved in synaptic transmission / dopamine metabolic process / positive regulation of DNA binding / positive regulation of mitochondrial fission / regulation of dopamine secretion / ubiquitin-specific protease binding / negative regulation of release of cytochrome c from mitochondria / startle response / protein monoubiquitination / cullin family protein binding / phospholipase binding / protein K63-linked ubiquitination / regulation of protein ubiquitination / mitophagy / regulation of glucose metabolic process / negative regulation of reactive oxygen species metabolic process / cellular response to unfolded protein / proteasomal protein catabolic process / cellular response to manganese ion / negative regulation of insulin secretion / protein K48-linked ubiquitination / protein autoubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ERAD pathway / ubiquitin ligase complex / heat shock protein binding / Hsp70 protein binding / PINK1-PRKN Mediated Mitophagy / tubulin binding / response to endoplasmic reticulum stress / adult locomotory behavior / Josephin domain DUBs / negative regulation of protein phosphorylation / regulation of mitochondrial membrane potential / mitochondrion organization / learning / ubiquitin binding / regulation of autophagy / synaptic transmission, glutamatergic / central nervous system development / G protein-coupled receptor binding / PDZ domain binding / macroautophagy / protein destabilization / regulation of protein stability / negative regulation of canonical Wnt signaling pathway 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Wauer, T. / Komander, D. | ||||||
![]() | ![]() タイトル: Structure of the Human Parkin Ligase Domain in an Autoinhibited State. 著者: Wauer, T. / 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 | ![]() | 133.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 104.4 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-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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Components on special symmetry positions |
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要素
#1: タンパク質 | 分子量: 36821.051 Da / 分子数: 1 / 断片: UPD AND RBR DOMAIN, RESIDUES 137-465 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: O60260, 合成酵素; C-N結合を形成; 酸-D-アミノ酸リガーゼ(ペプチド合成) | ||||||
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#2: 化合物 | ChemComp-ZN / #3: 化合物 | #4: 化合物 | ChemComp-GOL / | #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: 3 Å3/Da / 溶媒含有率: 58.8 % / 解説: NONE |
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結晶化 | pH: 7 詳細: 1.6 M LITHIUM SULPHATE, 10 MM MAGNESIUM CHLORIDE, 50 MM MES (PH 5.4) |
-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 PIXEL / 検出器: PIXEL / 日付: 2013年2月10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: 1 Å / 相対比: 1 |
反射 | 解像度: 2.25→58.33 Å / Num. obs: 24502 / % possible obs: 98 % / Observed criterion σ(I): 2 / 冗長度: 5 % / Biso Wilson estimate: 42.75 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.3 |
反射 シェル | 解像度: 2.25→2.37 Å / 冗長度: 5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / % possible all: 99.1 |
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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: NONE 解像度: 2.25→48.619 Å / SU ML: 0.21 / σ(F): 1.34 / 位相誤差: 23.6 / 立体化学のターゲット値: ML
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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 / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.25→48.619 Å
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拘束条件 |
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LS精密化 シェル |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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