+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-6482 | |||||||||
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タイトル | Cryo-electron microscopy of alpha Synuclein amyloid fibrils | |||||||||
マップデータ | Extruded 2D reconstruction of in vitro assembled alpha Synuclein amyoid fibrils | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 protein binding / 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 ...protein binding / 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 macrophage activation / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / mitochondrial ATP synthesis coupled electron transport / negative regulation of microtubule polymerization / synaptic vesicle transport / dynein complex binding / positive regulation of receptor recycling / regulation of dopamine secretion / positive regulation of endocytosis / 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 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / kinesin binding / alpha-tubulin binding / regulation of presynapse assembly / synaptic vesicle endocytosis / negative regulation of serotonin uptake / 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 / response to interleukin-1 / adult locomotory behavior / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / fatty acid metabolic process / long-term synaptic potentiation / fatty acid binding / regulation of transmembrane transporter activity / ferrous iron binding / synapse organization / phospholipid binding / protein tetramerization / phosphoprotein binding / microglial cell activation / regulation of long-term neuronal synaptic plasticity / negative regulation of protein kinase activity / tau protein binding / protein destabilization / PKR-mediated signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / actin binding / 細胞皮質 / histone binding / 成長円錐 / chemical synaptic transmission / postsynapse / neuron apoptotic process / negative regulation of neuron apoptotic process / amyloid fibril formation / response to lipopolysaccharide / リソソーム / molecular adaptor activity 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 40.0 Å | |||||||||
データ登録者 | Dearborn AD / Wall JS / Cheng N / Heymann JB / Kajava AV / Varkey J / Langen R / Steven AC | |||||||||
引用 | ジャーナル: J Biol Chem / 年: 2016 タイトル: α-Synuclein Amyloid Fibrils with Two Entwined, Asymmetrically Associated Protofibrils. 著者: Altaira D Dearborn / Joseph S Wall / Naiqian Cheng / J Bernard Heymann / Andrey V Kajava / Jobin Varkey / Ralf Langen / Alasdair C Steven / 要旨: Parkinson disease and other progressive neurodegenerative conditions are characterized by the intracerebral presence of Lewy bodies, containing amyloid fibrils of α-synuclein. We used cryo-electron ...Parkinson disease and other progressive neurodegenerative conditions are characterized by the intracerebral presence of Lewy bodies, containing amyloid fibrils of α-synuclein. We used cryo-electron microscopy and scanning transmission electron microscopy (STEM) to study in vitro-assembled fibrils. These fibrils are highly polymorphic. Focusing on twisting fibrils with an inter-crossover spacing of 77 nm, our reconstructions showed them to consist of paired protofibrils. STEM mass per length data gave one subunit per 0.47 nm axial rise per protofibril, consistent with a superpleated β-structure. The STEM images show two thread-like densities running along each of these fibrils, which we interpret as ladders of metal ions. These threads confirmed the two-protofibril architecture of the 77-nm twisting fibrils and allowed us to identify this morphotype in STEM micrographs. Some other, but not all, fibril morphotypes also exhibit dense threads, implying that they also present a putative metal binding site. We propose a molecular model for the protofibril and suggest that polymorphic variant fibrils have different numbers of protofibrils that are associated differently. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_6482.map.gz | 13.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-6482-v30.xml emd-6482.xml | 11.1 KB 11.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_6482.png | 54.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-6482 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6482 | HTTPS FTP |
-関連構造データ
類似構造データ |
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-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_6482.map.gz / 形式: CCP4 / 大きさ: 14.4 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Extruded 2D reconstruction of in vitro assembled alpha Synuclein amyoid fibrils | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : In vitro assembled, recombinant amyloid fibrils of full-length hu...
全体 | 名称: In vitro assembled, recombinant amyloid fibrils of full-length human alpha Synuclein |
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要素 |
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-超分子 #1000: In vitro assembled, recombinant amyloid fibrils of full-length hu...
超分子 | 名称: In vitro assembled, recombinant amyloid fibrils of full-length human alpha Synuclein タイプ: sample / ID: 1000 / 詳細: The sample was morphologically heterogeneous. / 集合状態: dimeric asymmetric unit / Number unique components: 2 |
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分子量 | 手法: Dark-field scanning transmission electron microscopy 59.1 MDa/micron compared to 61.5 MDa/micron theoretical weight |
-分子 #1: alpha Synuclein
分子 | 名称: alpha Synuclein / タイプ: protein_or_peptide / ID: 1 / Name.synonym: NACP, PARK1 / 集合状態: Amyloid / 組換発現: Yes |
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由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: Human / 組織: Brain / 細胞: Neuron / 細胞中の位置: Lewy Body |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) / 組換株: BL21*(DE3)pLysS / 組換プラスミド: pRK172aS |
配列 | UniProtKB: Α-シヌクレイン GO: magnesium ion binding, fatty acid binding, copper ion binding, calcium ion binding, protein binding InterPro: Α-シヌクレイン |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | らせん対称体再構成法 |
試料の集合状態 | filament |
-試料調製
濃度 | 4 mg/mL |
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緩衝液 | pH: 7.4 / 詳細: 10 mM HEPES, 100 mM NaCl, 0.1% NaN3 |
グリッド | 詳細: R1.2/1.3 400 mesh copper Quantifoil grid, glow-discharged in argon/oxygen |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / チャンバー内温度: 90 K / 装置: LEICA KF80 / 手法: Manually blotted before plunging |
-電子顕微鏡法
顕微鏡 | FEI/PHILIPS CM200FEG |
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電子線 | 加速電圧: 120 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 51840 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / 最大 デフォーカス(公称値): 3.5 µm / 最小 デフォーカス(公称値): 2.0 µm / 倍率(公称値): 50000 |
試料ステージ | 試料ホルダーモデル: GATAN LIQUID NITROGEN |
日付 | 2012年6月5日 |
撮影 | カテゴリ: FILM / フィルム・検出器のモデル: KODAK SO-163 FILM デジタル化 - スキャナー: NIKON SUPER COOLSCAN 9000 デジタル化 - サンプリング間隔: 6.35 µm / 実像数: 110 / 平均電子線量: 15 e/Å2 / ビット/ピクセル: 16 |
-画像解析
CTF補正 | 詳細: phase-flipped micrograph |
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最終 再構成 | 想定した対称性 - らせんパラメータ - Δz: 4.7 Å 想定した対称性 - らせんパラメータ - ΔΦ: 1.1 ° 想定した対称性 - らせんパラメータ - 軸対称性: C1 (非対称) 解像度のタイプ: BY AUTHOR / 解像度: 40.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Bsoft 詳細: Extruded from a 2D reconstruction based upon helical parameters |
詳細 | The 2D reconstructions were made and aligned using bhelcross. The helical parameters were determined per fibril in real space and imposed on the average using bhelcross. |