+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3q28 | |||||||||
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タイトル | Cyrstal structure of human alpha-synuclein (58-79) fused to maltose binding protein (MBP) | |||||||||
要素 | Maltose-binding periplasmic protein/alpha-synuclein chimeric protein | |||||||||
キーワード | SUGAR BINDING PROTEIN / PROTEIN FIBRIL / fusion protein (融合タンパク質) / amyloid (アミロイド) | |||||||||
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 / negative regulation of chaperone-mediated autophagy / mitochondrial membrane organization / 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 / dopamine biosynthetic process / SNARE complex assembly / positive regulation of neurotransmitter secretion / synaptic vesicle priming / dopamine uptake involved in synaptic transmission / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / regulation of macrophage activation / mitochondrial ATP synthesis coupled electron transport / negative regulation of microtubule polymerization / synaptic vesicle transport / dynein complex binding / positive regulation of receptor recycling / detection of maltose stimulus / regulation of dopamine secretion / maltose binding / maltose transport complex / protein kinase inhibitor activity / maltose transport / negative regulation of thrombin-activated receptor signaling pathway / maltodextrin transmembrane transport / response to type II interferon / cuprous ion binding / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / kinesin binding / regulation of presynapse assembly / alpha-tubulin binding / synaptic vesicle endocytosis / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of serotonin uptake / carbohydrate transport / localization / phospholipid metabolic process / supramolecular fiber organization / axon terminus / 封入体 / cellular response to copper ion / Hsp70 protein binding / cellular response to epinephrine stimulus / excitatory postsynaptic potential / ATP-binding cassette (ABC) transporter complex / response to interleukin-1 / cell chemotaxis / adult locomotory behavior / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / fatty acid metabolic process / long-term synaptic potentiation / regulation of transmembrane transporter activity / ferrous iron binding / protein tetramerization / synapse organization / phosphoprotein binding / regulation of long-term neuronal synaptic plasticity / microglial cell activation / negative regulation of protein kinase activity / phospholipid binding / protein destabilization / PKR-mediated signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / tau protein binding / positive regulation of protein serine/threonine kinase activity / receptor internalization / synaptic vesicle membrane / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / マイクロフィラメント / positive regulation of peptidyl-serine phosphorylation / cellular response to oxidative stress / outer membrane-bounded periplasmic space / actin binding / 細胞皮質 / 成長円錐 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli (大腸菌) Homo sapiens (ヒト) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.6 Å | |||||||||
データ登録者 | Zhao, M. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. | |||||||||
引用 | ジャーナル: Protein Sci. / 年: 2011 タイトル: Structures of segments of alpha-synuclein fused to maltose-binding protein suggest intermediate states during amyloid formation 著者: Zhao, M. / Cascio, D. / Sawaya, M.R. / Eisenberg, D. | |||||||||
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 | 3q28.cif.gz | 176.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3q28.ent.gz | 137.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3q28.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/q2/3q28 ftp://data.pdbj.org/pub/pdb/validation_reports/q2/3q28 | 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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-要素
#1: タンパク質 | 分子量: 42900.461 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Escherichia coli (大腸菌), (組換発現) Homo sapiens (ヒト) 遺伝子: SNCA / プラスミド: pMAL-C2X / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: P0AEX9, UniProt: P37840 | ||
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#2: 多糖 | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | ||
#3: 化合物 | ChemComp-SO4 / #4: 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: 1.88 Å3/Da / 溶媒含有率: 34.54 % |
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結晶化 | 温度: 290 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 9 詳細: 0.1M BICINE pH 9.0, 3.2 M AMMONIUM SULFATE, vapor diffusion, hanging drop, temperature 290K |
-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-C / 波長: 0.97949 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2010年7月25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: 0.97949 Å / 相対比: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 1.6→19.632 Å / Num. obs: 42173 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.459 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.74 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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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: PDB ENTRY 1ANF 解像度: 1.6→19.632 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.9048 / SU ML: 0.16 / σ(F): 1.99 / 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: 1.06 Å / VDWプローブ半径: 1.3 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 34.427 Å2 / ksol: 0.39 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 77.18 Å2 / Biso mean: 17.5407 Å2 / Biso min: 5.45 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.6→19.632 Å
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拘束条件 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %
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精密化 TLS | 手法: refined / Origin x: -9.9416 Å / Origin y: 6.9732 Å / Origin z: -12.8454 Å
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精密化 TLSグループ |
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