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基本情報
登録情報 | データベース: PDB / ID: 7fb9 | ||||||
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タイトル | Crystal Structure of Human Cu, Zn Superoxide Dismutase (SOD1) | ||||||
![]() | Superoxide dismutase [Cu-Zn] | ||||||
![]() | OXIDOREDUCTASE / Superoxide / oxidation / metalloprotein / hydrogen peroxide / filament / ALS | ||||||
機能・相同性 | ![]() action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / retrograde axonal transport / anterograde axonal transport / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / retrograde axonal transport / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of protein kinase activity / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / negative regulation of cholesterol biosynthetic process / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / positive regulation of catalytic activity / muscle cell cellular homeostasis / regulation of GTPase activity / heart contraction / superoxide metabolic process / superoxide dismutase / negative regulation of reproductive process / Detoxification of Reactive Oxygen Species / negative regulation of developmental process / transmission of nerve impulse / superoxide dismutase activity / : / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / positive regulation of superoxide anion generation / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / placenta development / locomotory behavior / determination of adult lifespan / sensory perception of sound / regulation of blood pressure / negative regulation of inflammatory response / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / Platelet degranulation / peroxisome / protein-folding chaperone binding / gene expression / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Baek, Y. / Ha, N.-C. | ||||||
資金援助 | 1件
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![]() | ![]() タイトル: Structural analysis of the overoxidized Cu/Zn-superoxide dismutase in ROS-induced ALS filament formation. 著者: Baek, Y. / Woo, T.G. / Ahn, J. / Lee, D. / Kwon, Y. / Park, B.J. / Ha, N.C. | ||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 437.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 284.8 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
関連構造データ | ![]() 7fb6C ![]() 1pu0S S: 精密化の開始モデル C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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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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詳細 | Chain M and N seem to be abnormal monomer SOD1. Some of the SOD1 proteins seem to be partially disordered, and cannot make a dimer in the soluble state. The chain M or N is a partially disordered protein and attached to the normal protein complexes. As a result, they have weak and diffused electron density maps and they don't have dimeric partners. |
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要素
#1: タンパク質 | 分子量: 16706.570 Da / 分子数: 14 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: 化合物 | ChemComp-ZN / #3: 化合物 | ChemComp-CU / #4: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | N | |
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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: 3.45 Å3/Da / 溶媒含有率: 64.38 % |
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結晶化 | 温度: 287.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 詳細: 0.1M sodium acetate-HCl (pH 4.5), 21% (w/v) PEG 3350 |
-データ収集
回折 | 平均測定温度: 100.15 K / Serial crystal experiment: N |
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放射光源 | 由来: ![]() ![]() |
検出器 | タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2020年8月1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: 0.97942 Å / 相対比: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.24 |
反射 | 解像度: 2.7→50 Å / Num. obs: 76247 / % possible obs: 93.8 % / 冗長度: 4.9 % / CC1/2: 0.944 / CC star: 0.986 / Rpim(I) all: 0.067 / Χ2: 0.953 / Net I/σ(I): 8.3 |
反射 シェル | 解像度: 2.7→2.75 Å / Mean I/σ(I) obs: 3.083 / Num. unique obs: 3191 / CC1/2: 0.416 / CC star: 0.767 / Rpim(I) all: 0.157 / Rrim(I) all: 0.294 |
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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: 1PU0 解像度: 2.7→49.52 Å / 交差検証法: FREE R-VALUE / σ(F): 1101.29 / 位相誤差: 32.1254 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 41.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.7→49.52 Å
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拘束条件 |
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LS精密化 シェル |
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