+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4r0w | ||||||
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タイトル | Vvtgvta, an amyloid forming segment from alpha synuclein, residues 70-76 | ||||||
要素 | Alpha-synuclein | ||||||
キーワード | PROTEIN FIBRIL / amyloid-like protofibril | ||||||
機能・相同性 | 機能・相同性情報 negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of transporter activity / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / response to iron(II) ion / regulation of norepinephrine uptake / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / regulation of macrophage activation / negative regulation of microtubule polymerization / synaptic vesicle transport / dopamine uptake involved in synaptic transmission / dynein complex binding / regulation of dopamine secretion / positive regulation of receptor recycling / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / response to type II interferon / cuprous ion binding / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / kinesin binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / synaptic vesicle endocytosis / regulation of presynapse assembly / negative regulation of serotonin uptake / alpha-tubulin binding / phospholipid metabolic process / supramolecular fiber organization / axon terminus / mitochondrial ATP synthesis coupled electron transport / inclusion body / fatty acid metabolic process / cellular response to copper ion / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / adult locomotory behavior / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / excitatory postsynaptic potential / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / regulation of transmembrane transporter activity / synapse organization / microglial cell activation / negative regulation of protein kinase activity / regulation of long-term neuronal synaptic plasticity / protein destabilization / ferrous iron binding / tau protein binding / positive regulation of protein serine/threonine kinase activity / PKR-mediated signaling / receptor internalization / phospholipid binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / synaptic vesicle membrane / positive regulation of inflammatory response / positive regulation of peptidyl-serine phosphorylation / actin cytoskeleton / actin binding / cellular response to oxidative stress / histone binding / cell cortex / growth cone / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / transcription cis-regulatory region binding / postsynapse / amyloid fibril formation / response to lipopolysaccharide / molecular adaptor activity / oxidoreductase activity / lysosome / response to xenobiotic stimulus 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: 1.5 Å | ||||||
データ登録者 | Ivanova, M.I. / Eisenberg, D.S. / Sawaya, M.R. | ||||||
引用 | ジャーナル: J.Am.Chem.Soc. / 年: 2014 タイトル: Structure-based design of functional amyloid materials. 著者: Li, D. / Jones, E.M. / Sawaya, M.R. / Furukawa, H. / Luo, F. / Ivanova, M. / Sievers, S.A. / Wang, W. / Yaghi, O.M. / Liu, C. / 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 | 4r0w.cif.gz | 8.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4r0w.ent.gz | 5.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4r0w.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 | 4r0w_validation.pdf.gz | 376.2 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4r0w_full_validation.pdf.gz | 376.2 KB | 表示 | |
XML形式データ | 4r0w_validation.xml.gz | 2.3 KB | 表示 | |
CIF形式データ | 4r0w_validation.cif.gz | 2.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/r0/4r0w ftp://data.pdbj.org/pub/pdb/validation_reports/r0/4r0w | 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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単位格子 |
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Components on special symmetry positions |
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詳細 | The biological unit is a fibril, comprising a pair of beta sheets constructed from chain A and unit cell translations along the b direction (that is, the b direction corresponds to the fiber axis) (i.e. X,Y,Z; X,Y+1,Z; X,Y+2,Z; etc.) together with a symmetry related sheet formed from 1/2-X,1/2+Y,-Z+1 and its unit cell translations along the b direction (i.e. 1/2-X,3/2+Y,-Z+1; 1/2-X,5/2+Y,-Z+1; etc.). REMARK 350 displays 5 strands from each sheet. |
-要素
#1: タンパク質・ペプチド | 分子量: 645.745 Da / 分子数: 1 / 断片: UNP RESIDUES 70-76 / 由来タイプ: 合成 詳細: VVTGVTA (residues 70-76) from Human alpha-synuclein, synthesized 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P37840 |
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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: 1.4 Å3/Da / 溶媒含有率: 12.42 % / Mosaicity: 0.6 ° |
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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: 6.5 詳細: isopropanol, sodium cacodylate, pH 6.5, 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: ESRF / ビームライン: ID13 / 波長: 0.895432 Å | ||||||||||||||||||||||||||||||||||||
検出器 | タイプ: MAR CCD 165 mm / 検出器: CCD / 日付: 2007年7月14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: 0.895432 Å / 相対比: 1 | ||||||||||||||||||||||||||||||||||||
反射 | 解像度: 1.5→90 Å / Num. all: 650 / Num. obs: 650 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / 冗長度: 3.1 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.193 / Χ2: 1.113 / Net I/σ(I): 5 | ||||||||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1 / Rejects: _
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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 開始モデル: ideal beta strand 解像度: 1.5→23.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.3048 / WRfactor Rwork: 0.274 / FOM work R set: 0.7168 / SU B: 3.234 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1311 / SU Rfree: 0.1219 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.122 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE 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: 1.4 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 39.73 Å2 / Biso mean: 11.91 Å2 / Biso min: 12.85 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.5→23.97 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.502→1.678 Å / Total num. of bins used: 5
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