+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3851 | |||||||||
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タイトル | Near-atomic resolution fibril structure of complete amyloid-beta(1-42) by cryo-EM | |||||||||
マップデータ | The density map was sharpened by a B-factor of -50 Ang^2 and filtered to 3.5 Ang. This density map was used for model building and refinement. | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis ...regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / regulation of Wnt signaling pathway / mating behavior / positive regulation of amyloid fibril formation / 繊毛 / Lysosome Vesicle Biogenesis / PTB domain binding / neuron remodeling / Golgi-associated vesicle / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / presynaptic active zone / nuclear envelope lumen / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / 小胞体 / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / negative regulation of long-term synaptic potentiation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / regulation of presynapse assembly / The NLRP3 inflammasome / intracellular copper ion homeostasis / transition metal ion binding / regulation of multicellular organism growth / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / クラスリン / Notchシグナリング / cholesterol metabolic process / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / neuron projection maintenance / positive regulation of glycolytic process / extracellular matrix organization / response to interleukin-1 / positive regulation of mitotic cell cycle / 軸索誘導 / adult locomotory behavior / dendritic shaft / trans-Golgi network membrane / locomotory behavior / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation / 学習 / positive regulation of interleukin-1 beta production / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / endosome lumen / Post-translational protein phosphorylation / synapse organization / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / neuromuscular junction / visual learning / serine-type endopeptidase inhibitor activity / recycling endosome / 認識 / positive regulation of inflammatory response / positive regulation of interleukin-6 production / neuron cellular homeostasis / Golgi lumen / エンドサイトーシス / positive regulation of non-canonical NF-kappaB signal transduction / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / neuron projection development / positive regulation of DNA-binding transcription factor activity / G2/M transition of mitotic cell cycle / cell-cell junction / シナプス小胞 / positive regulation of tumor necrosis factor production / regulation of translation 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: 4.0 Å | |||||||||
データ登録者 | Gremer L / Schoelzel D / Schenk C / Reinartz E / Labahn J / Ravelli R / Tusche M / Lopez-Iglesias C / Hoyer W / Heise H ...Gremer L / Schoelzel D / Schenk C / Reinartz E / Labahn J / Ravelli R / Tusche M / Lopez-Iglesias C / Hoyer W / Heise H / Willbold D / Schroeder GF | |||||||||
引用 | ジャーナル: Science / 年: 2017 タイトル: Fibril structure of amyloid-β(1-42) by cryo-electron microscopy. 著者: Lothar Gremer / Daniel Schölzel / Carla Schenk / Elke Reinartz / Jörg Labahn / Raimond B G Ravelli / Markus Tusche / Carmen Lopez-Iglesias / Wolfgang Hoyer / Henrike Heise / Dieter Willbold ...著者: Lothar Gremer / Daniel Schölzel / Carla Schenk / Elke Reinartz / Jörg Labahn / Raimond B G Ravelli / Markus Tusche / Carmen Lopez-Iglesias / Wolfgang Hoyer / Henrike Heise / Dieter Willbold / Gunnar F Schröder / 要旨: Amyloids are implicated in neurodegenerative diseases. Fibrillar aggregates of the amyloid-β protein (Aβ) are the main component of the senile plaques found in brains of Alzheimer's disease ...Amyloids are implicated in neurodegenerative diseases. Fibrillar aggregates of the amyloid-β protein (Aβ) are the main component of the senile plaques found in brains of Alzheimer's disease patients. We present the structure of an Aβ(1-42) fibril composed of two intertwined protofilaments determined by cryo-electron microscopy (cryo-EM) to 4.0-angstrom resolution, complemented by solid-state nuclear magnetic resonance experiments. The backbone of all 42 residues and nearly all side chains are well resolved in the EM density map, including the entire N terminus, which is part of the cross-β structure resulting in an overall "LS"-shaped topology of individual subunits. The dimer interface protects the hydrophobic C termini from the solvent. The characteristic staggering of the nonplanar subunits results in markedly different fibril ends, termed "groove" and "ridge," leading to different binding pathways on both fibril ends, which has implications for fibril growth. | |||||||||
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_3851.map.gz | 36.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3851-v30.xml emd-3851.xml | 17.1 KB 17.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_3851_fsc.xml | 7.7 KB | 表示 | FSCデータファイル |
画像 | emd_3851.png | 147.8 KB | ||
その他 | emd_3851_half_map_1.map.gz emd_3851_half_map_2.map.gz | 13.5 MB 13.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3851 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3851 | HTTPS FTP |
-関連構造データ
-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_3851.map.gz / 形式: CCP4 / 大きさ: 38.4 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | The density map was sharpened by a B-factor of -50 Ang^2 and filtered to 3.5 Ang. This density map was used for model building and refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.935 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
-ハーフマップ: even half map.
ファイル | emd_3851_half_map_1.map | ||||||||||||
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注釈 | even half map. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: odd half map.
ファイル | emd_3851_half_map_2.map | ||||||||||||
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注釈 | odd half map. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Beta-amyloid protein 42 fibrils
全体 | 名称: Beta-amyloid protein 42 fibrilsアミロイドβ |
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要素 |
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-超分子 #1: Beta-amyloid protein 42 fibrils
超分子 | 名称: Beta-amyloid protein 42 fibrils / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Escherichia coli (大腸菌) |
-分子 #1: Amyloid beta A4 protein
分子 | 名称: Amyloid beta A4 protein / タイプ: protein_or_peptide / ID: 1 / コピー数: 9 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 4.520087 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IA |
-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
緩衝液 | pH: 2 構成要素:
詳細: in water | ||||||
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グリッド | モデル: UltrAuFoil R 1.2/1.3 Quantifoil / 材質: GOLD / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE | ||||||
凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK IV 詳細: 2.5 microL sample was applied to the grid, blotted for 2.5 s before plunging.. |
-電子顕微鏡法
顕微鏡 | FEI TECNAI ARCTICA |
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電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 倍率(公称値): 110000 |
撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 検出モード: INTEGRATING / 撮影したグリッド数: 1 / 実像数: 2026 / 平均露光時間: 2.0 sec. / 平均電子線量: 24.0 e/Å2 |
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |
-画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: AB INITIO MODEL 当てはまり具合の基準: Cross-correlation coefficient |
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得られたモデル | PDB-5oqv: |