+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4nio | ||||||
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タイトル | GVTGIAQ segment 147-153 from Human Superoxide Dismutase with I149T mutation associated with a familial form of amyotrophic lateral sclerosis | ||||||
要素 | GVTGIAQ segment from Superoxide dismutase [Cu-Zn] | ||||||
キーワード | PROTEIN FIBRIL / steric zipper / cross-beta spine / amyloid fiber | ||||||
機能・相同性 | 機能・相同性情報 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 | Homo Sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.3 Å | ||||||
データ登録者 | Sievers, S.A. / Sawaya, M.R. / Eisenberg, D. / Ivanova, M.I. | ||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2014 タイトル: Aggregation-triggering segments of SOD1 fibril formation support a common pathway for familial and sporadic ALS. 著者: Ivanova, M.I. / Sievers, S.A. / Guenther, E.L. / Johnson, L.M. / Winkler, D.D. / Galaleldeen, A. / Sawaya, M.R. / Hart, P.J. / Eisenberg, D.S. | ||||||
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 | 4nio.cif.gz | 9.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4nio.ent.gz | 5.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4nio.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ni/4nio ftp://data.pdbj.org/pub/pdb/validation_reports/ni/4nio | HTTPS FTP |
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-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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単位格子 |
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詳細 | biological unit is a pair of beta-sheets. One sheet is composed of symmetry operators X,Y,Z; X,Y-1,Z; X,Y+1,Z; X,Y-2,Z; X,Y+2,Z, etc.: the opposing sheet is composed of symmetry operators 1/2-x,1/2+y,-z; 1/2-x,-1/2+y,-z; 1/2-x, 3/2+y,-z; 1/2-x,-3/2+y,-z; 1/2-x, 5/2+y,-z, etc. |
-要素
#1: タンパク質・ペプチド | 分子量: 644.718 Da / 分子数: 1 / 断片: UNP Residues 148-154 / 変異: I149T / 由来タイプ: 合成 / 由来: (合成) Homo Sapiens (ヒト) / 参照: UniProt: P00441 |
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#2: 水 | ChemComp-HOH / |
-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: 1.48 Å3/Da / 溶媒含有率: 16.89 % |
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.5 詳細: 0.1 M sodium acetate pH 4.5, 0.7 M hexanediol, vapor diffusion, hanging drop, temperature 298K |
-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: シンクロトロン / サイト: APS / ビームライン: 24-ID-E / 波長: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2011年3月3日 / 詳細: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
放射 | モノクロメーター: cryogenically-cooled single crystal Si(220) 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: 0.9792 Å / 相対比: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 1.3→100 Å / Num. all: 1053 / Num. obs: 1053 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / 冗長度: 4.3 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.128 / Χ2: 1.042 / Net I/σ(I): 11 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル |
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-位相決定
位相決定 | 手法: 分子置換 | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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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: 分子置換 / 解像度: 1.3→22.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2247 / WRfactor Rwork: 0.2221 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7612 / SU B: 1.39 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0712 / SU Rfree: 0.0731 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.073 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 1.4 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 31.56 Å2 / Biso mean: 9.1706 Å2 / Biso min: 5.33 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.3→22.54 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.301→1.335 Å / Total num. of bins used: 20
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