+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5aef | ||||||
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タイトル | Electron cryo-microscopy of an Abeta(1-42)amyloid fibril | ||||||
要素 | AMYLOID BETA A4 PROTEIN | ||||||
キーワード | PROTEIN FIBRIL / ALZHEIMER'S DISEASE / AMYLOID FIBRIL / PROTEIN AGGREGATION / PROTEIN FOLDING / CROSS-BETA / FREALIX | ||||||
機能・相同性 | 機能・相同性情報 cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / signaling receptor activator activity / axon midline choice point recognition ...cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / signaling receptor activator activity / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / Lysosome Vesicle Biogenesis / ciliary rootlet / PTB domain binding / Golgi-associated vesicle / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / dendrite development / presynaptic active zone / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / The NLRP3 inflammasome / transition metal ion binding / regulation of presynapse assembly / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / negative regulation of neuron differentiation / intracellular copper ion homeostasis / ECM proteoglycans / trans-Golgi network membrane / positive regulation of T cell migration / smooth endoplasmic reticulum / spindle midzone / Purinergic signaling in leishmaniasis infection / clathrin-coated pit / protein serine/threonine kinase binding / positive regulation of chemokine production / regulation of peptidyl-tyrosine phosphorylation / forebrain development / Notch signaling pathway / neuron projection maintenance / Mitochondrial protein degradation / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / positive regulation of calcium-mediated signaling / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / cholesterol metabolic process / response to interleukin-1 / positive regulation of mitotic cell cycle / extracellular matrix organization / axonogenesis / adult locomotory behavior / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-1 beta production / dendritic shaft / learning / cognition / positive regulation of long-term synaptic potentiation / central nervous system development / endosome lumen / locomotory behavior / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / microglial cell activation / synapse organization / serine-type endopeptidase inhibitor activity / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / visual learning / neuromuscular junction / recycling endosome / positive regulation of interleukin-6 production / Golgi lumen / neuron cellular homeostasis / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / G2/M transition of mitotic cell cycle / cell-cell junction / neuron projection development / Platelet degranulation / apical part of cell / synaptic vesicle 類似検索 - 分子機能 | ||||||
生物種 | HOMO SAPIENS (ヒト) | ||||||
手法 | 電子顕微鏡法 / らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 5 Å | ||||||
データ登録者 | Schmidt, M. / Rohou, A. / Lasker, K. / Yadav, J.K. / Schiene-Fischer, C. / Fandrich, M. / Grigorieff, N. | ||||||
引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2015 タイトル: Peptide dimer structure in an Aβ(1-42) fibril visualized with cryo-EM. 著者: Matthias Schmidt / Alexis Rohou / Keren Lasker / Jay K Yadav / Cordelia Schiene-Fischer / Marcus Fändrich / Nikolaus Grigorieff / 要旨: Alzheimer's disease (AD) is a fatal neurodegenerative disorder in humans and the main cause of dementia in aging societies. The disease is characterized by the aberrant formation of β-amyloid (Aβ) ...Alzheimer's disease (AD) is a fatal neurodegenerative disorder in humans and the main cause of dementia in aging societies. The disease is characterized by the aberrant formation of β-amyloid (Aβ) peptide oligomers and fibrils. These structures may damage the brain and give rise to cerebral amyloid angiopathy, neuronal dysfunction, and cellular toxicity. Although the connection between AD and Aβ fibrillation is extensively documented, much is still unknown about the formation of these Aβ aggregates and their structures at the molecular level. Here, we combined electron cryomicroscopy, 3D reconstruction, and integrative structural modeling methods to determine the molecular architecture of a fibril formed by Aβ(1-42), a particularly pathogenic variant of Aβ peptide. Our model reveals that the individual layers of the Aβ fibril are formed by peptide dimers with face-to-face packing. The two peptides forming the dimer possess identical tilde-shaped conformations and interact with each other by packing of their hydrophobic C-terminal β-strands. The peptide C termini are located close to the main fibril axis, where they produce a hydrophobic core and are surrounded by the structurally more flexible and charged segments of the peptide N termini. The observed molecular architecture is compatible with the general chemical properties of Aβ peptide and provides a structural basis for various biological observations that illuminate the molecular underpinnings of AD. Moreover, the structure provides direct evidence for a steric zipper within a fibril formed by full-length Aβ peptide. | ||||||
履歴 |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 3-STRANDED BARREL THIS IS REPRESENTED BY A 4-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 5aef.cif.gz | 30.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5aef.ent.gz | 22.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5aef.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 | 5aef_validation.pdf.gz | 603.6 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5aef_full_validation.pdf.gz | 610.1 KB | 表示 | |
XML形式データ | 5aef_validation.xml.gz | 13.7 KB | 表示 | |
CIF形式データ | 5aef_validation.cif.gz | 19.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ae/5aef ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5aef | HTTPS FTP |
-関連構造データ
関連構造データ | 3132MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質・ペプチド | 分子量: 2835.365 Da / 分子数: 2 / 断片: ABETA, UNP RESIDUES 630-657 / 由来タイプ: 合成 / 由来: (合成) HOMO SAPIENS (ヒト) / 参照: UniProt: E9PG40, UniProt: P05067*PLUS |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: FILAMENT / 3次元再構成法: らせん対称体再構成法 |
-試料調製
構成要素 | 名称: ABETA(1-42) AMYLOID-LIKE FIBRIL / タイプ: COMPLEX / 詳細: FIBRIL |
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緩衝液 | 名称: 50MM TRIS-HCL / pH: 7.4 / 詳細: 50MM TRIS-HCL |
試料 | 濃度: 1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: HOLEY CARBON |
急速凍結 | 装置: GATAN CRYOPLUNGE 3 / 凍結剤: ETHANE / 詳細: 4 SEC BACKSIDE BLOTTING |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai F30 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F30 / 日付: 2010年2月5日 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 59000 X / 倍率(補正後): 58333 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1750 nm / Cs: 2 mm |
試料ホルダ | 温度: 100 K |
撮影 | 電子線照射量: 30 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
画像スキャン | デジタル画像の数: 29 |
-解析
EMソフトウェア | 名称: FREALIX / カテゴリ: 3次元再構成 | ||||||||||||
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CTF補正 | 詳細: INDIVIDUAL HELICAL SUBUNITS | ||||||||||||
3次元再構成 | 手法: PROJECTION MATCHING AND FOURIER INVERSION / 解像度: 5 Å / 粒子像の数: 62320 / ピクセルサイズ(実測値): 1.2 Å 詳細: FINAL MAP WAS CALCULATED FROM 29 SINGLE FILAMENT RECONSTRUCTIONS. DATA USED FOR REFINEMENT WAS NEVER BELOW 10 ANGSTROM RESOLUTION. RESOLUTION OF FIBRIL CORE IS ABOUT 5 ANGSTROM. 3 POSSIBLE ...詳細: FINAL MAP WAS CALCULATED FROM 29 SINGLE FILAMENT RECONSTRUCTIONS. DATA USED FOR REFINEMENT WAS NEVER BELOW 10 ANGSTROM RESOLUTION. RESOLUTION OF FIBRIL CORE IS ABOUT 5 ANGSTROM. 3 POSSIBLE MODELS FOR THE CENTRAL REGION OF A ABETA(1-42) FIBRIL RECONSTRUCTION. MODEL1 ABETA(17-42) MODEL2 ABETA( 16-41) MODEL3 ABETA(15-40) SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3132. (DEPOSITION ID: 13698). 対称性のタイプ: HELICAL | ||||||||||||
原子モデル構築 | プロトコル: OTHER / 空間: REAL / Target criteria: ELECTRON DENSITY / 詳細: METHOD--DIREX REFINEMENT PROTOCOL--PEPTIDE CHAIN | ||||||||||||
精密化 | 最高解像度: 5 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 5 Å
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