+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4r0u | ||||||
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タイトル | Tgvtava, an amyloid forming segment from alpha synuclein, residues 72-78 | ||||||
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 regulation of phospholipase activity / negative regulation of monooxygenase activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / positive regulation of glutathione peroxidase activity / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process ...regulation of phospholipase activity / negative regulation of monooxygenase activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / positive regulation of glutathione peroxidase activity / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / 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 / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of protein localization to cell periphery / 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 / regulation of dopamine secretion / dynein complex binding / 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 / response to magnesium ion / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / kinesin binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitochondrial ATP synthesis coupled electron transport / synaptic vesicle endocytosis / regulation of presynapse assembly / negative regulation of serotonin uptake / alpha-tubulin binding / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / : / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / excitatory postsynaptic potential / SNARE binding / fatty acid metabolic process / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / regulation of transmembrane transporter activity / protein destabilization / negative regulation of protein kinase activity / microglial cell activation / regulation of long-term neuronal synaptic plasticity / synapse organization / ferrous iron binding / positive regulation of protein serine/threonine kinase activity / tau protein binding / PKR-mediated signaling / receptor internalization / phospholipid binding / : / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / actin binding / cell cortex / cellular response to oxidative stress / histone binding / growth cone / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynapse / response to lipopolysaccharide / amyloid fibril formation / molecular adaptor activity / lysosome / oxidoreductase activity / transcription cis-regulatory region binding / positive regulation of apoptotic process 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: 1.38 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 | 4r0u.cif.gz | 8.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4r0u.ent.gz | 5.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4r0u.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 | 4r0u_validation.pdf.gz | 403.9 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4r0u_full_validation.pdf.gz | 403.9 KB | 表示 | |
XML形式データ | 4r0u_validation.xml.gz | 2.4 KB | 表示 | |
CIF形式データ | 4r0u_validation.cif.gz | 2.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/r0/4r0u ftp://data.pdbj.org/pub/pdb/validation_reports/r0/4r0u | 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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単位格子 |
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詳細 | There are two choices of the biological unit. The first choice is a pair of indefinitely long 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-X,Y+1/2,1-Z and its unit cell translations along the b direction (i.e. 1-x,y+3/2,1-z; 1-x,y+5/2,1-z, etc.). The second choice of biological unit is a pair of beta sheets constructed from chain A and unit cell translations along the b direction (i.e. X,Y,Z; X,Y+1,Z; X,Y+2,Z; etc.) together with a symmetry related sheet formed from -X,1/2+Y,1-Z and its unit cell translations along the b direction (i.e. -x,y+3/2,1-z; -x,y+5/2,1-z; etc.). REMARK 350 displays 5 strands from both sheets for the first choice. |
-要素
#1: タンパク質・ペプチド | 分子量: 617.692 Da / 分子数: 1 / 断片: UNP RESIDUES 72-78 / 由来タイプ: 合成 詳細: TGVTAVA (residues 72-78) 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: 1.52 Å3/Da / 溶媒含有率: 19.34 % / 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 詳細: 0.2M magnesium formate, 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13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: 1.38→90 Å / Num. all: 798 / Num. obs: 798 / % possible obs: 83.8 % / Observed criterion σ(I): -3 / 冗長度: 3.4 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.151 / Χ2: 1.125 / Net I/σ(I): 8.4 | ||||||||||||||||||||||||||||||||||||
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: 1.38→25.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.2528 / WRfactor Rwork: 0.2378 / FOM work R set: 0.7067 / SU B: 2.336 / SU ML: 0.077 / SU R Cruickshank DPI: 0.096 / SU Rfree: 0.0873 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.087 / 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: 41.77 Å2 / Biso mean: 16.624 Å2 / Biso min: 8.24 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.38→25.49 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.38→1.542 Å / Total num. of bins used: 5
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