EMDB-28740: Brain-derived 42-residue amyloid-beta fibril type A

基本情報

登録情報

データベース: EMDB / ID: EMD-28740

• タイトル: Brain-derived 42-residue amyloid-beta fibril type A

試料

• 複合体: amyloid-b 42 (Ab42) fibril
  • タンパク質・ペプチド: Beta-amyloid protein 42

• キーワード: amyloid-b 42 (Ab42) fibril / Alzheimer' / s disease (AD) / Polymorphism. / PROTEIN FIBRIL

機能・相同性

分子機能:

amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / regulation of synapse structure or activity / axon midline choice point recognition / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Lysosome Vesicle Biogenesis / astrocyte projection / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / dendrite development / positive regulation of protein metabolic process / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / The NLRP3 inflammasome / transition metal ion binding / main axon / regulation of multicellular organism growth / intracellular copper ion homeostasis / regulation of presynapse assembly / ECM proteoglycans / positive regulation of T cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / cellular response to manganese ion / Notch signaling pathway / clathrin-coated pit / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / protein serine/threonine kinase binding / cellular response to copper ion / platelet alpha granule lumen / cellular response to cAMP / positive regulation of glycolytic process / central nervous system development / positive regulation of interleukin-1 beta production / endosome lumen / dendritic shaft / trans-Golgi network membrane / adult locomotory behavior / positive regulation of long-term synaptic potentiation / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / microglial cell activation / serine-type endopeptidase inhibitor activity / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / regulation of long-term neuronal synaptic plasticity / cellular response to nerve growth factor stimulus / synapse organization / recycling endosome / visual learning / positive regulation of interleukin-6 production / response to lead ion / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endocytosis / cellular response to amyloid-beta / positive regulation of inflammatory response / neuron projection development / positive regulation of tumor necrosis factor production / Platelet degranulation / heparin binding / regulation of translation / regulation of gene expression / early endosome membrane / perikaryon / G alpha (i) signalling events / G alpha (q) signalling events / dendritic spine

ドメイン・相同性:

Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily

構成要素:

Amyloid-beta precursor protein

• 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: 2.83 Å
• データ登録者: Tycko R / Lee M / Yau Y-M / Louis JM

資金援助

米国, 1件

Organization	Grant number	国
Not funded		米国

• 引用: ジャーナル: Proc Natl Acad Sci U S A / 年: 2023; タイトル: Structures of brain-derived 42-residue amyloid-β fibril polymorphs with unusual molecular conformations and intermolecular interactions.; 著者: Myungwoon Lee / Wai-Ming Yau / John M Louis / Robert Tycko / ; 要旨: Fibrils formed by the 42-residue amyloid-β peptide (Aβ42), a main component of amyloid deposits in Alzheimer's disease (AD), are known to be polymorphic, i.e., to contain multiple possible molecular structures. Previous studies of Aβ42 fibrils, including fibrils prepared entirely in vitro or extracted from brain tissue and using solid-state NMR (ssNMR) or cryogenic electron microscopy (cryo-EM) methods, have found polymorphs with differences in amino acid sidechain orientations, lengths of structurally ordered segments, and contacts between cross-β subunit pairs within a single filament. Despite these differences, Aβ42 molecules adopt a common S-shaped conformation in all previously described high-resolution Aβ42 fibril structures. Here we report two cryo-EM-based structures of Aβ42 fibrils that are qualitatively different, in samples derived from AD brain tissue by seeded growth. In type A fibrils, residues 12 to 42 adopt a ν-shaped conformation, with both intra-subunit and intersubunit hydrophobic contacts to form a compact core. In type B fibrils, residues 2 to 42 adopt an υ-shaped conformation, with only intersubunit contacts and internal pores. Type A and type B fibrils have opposite helical handedness. Cryo-EM density maps and molecular dynamics simulations indicate intersubunit K16-A42 salt bridges in type B fibrils and partially occupied K28-A42 salt bridges in type A fibrils. The coexistence of two predominant polymorphs, with differences in N-terminal dynamics, is supported by ssNMR data, as is faithful propagation of structures from first-generation to second-generation brain-seeded Aβ42 fibril samples. These results demonstrate that Aβ42 fibrils can exhibit a greater range of structural variations than seen in previous studies.

履歴

登録	2022年10月31日	-
ヘッダ(付随情報) 公開	2023年3月22日	-
マップ公開	2023年3月22日	-
更新	2024年6月19日	-
現状	2024年6月19日	処理サイト: RCSB / 状態: 公開

マップ

• ファイル: ダウンロード / ファイル: emd_28740.map.gz / 形式: CCP4 / 大きさ: 476.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• ボクセルのサイズ: X=Y=Z: 0.86 Å

密度

表面レベル	登録者による: 0.009
最小 - 最大	-0.037047435 - 0.08876042
平均 (標準偏差)	0.0000097738 (±0.0015273857)

• 対称性: 空間群: 1

詳細

EMDB XML:

マップ形状	Axis order X Y Z Origin 0 0 0 サイズ 500 500 500 Spacing 500 500 500
セル	A=B=C: 430.0 Å α=β=γ: 90.0 °

添付データ

ハーフマップ: #1

• ファイル: emd_28740_half_map_1.map

ハーフマップ: #2

• ファイル: emd_28740_half_map_2.map

試料の構成要素

全体 : amyloid-b 42 (Ab42) fibril

• 全体: 名称: amyloid-b 42 (Ab42) fibril

要素

• 複合体: amyloid-b 42 (Ab42) fibril
  • タンパク質・ペプチド: Beta-amyloid protein 42

超分子 #1: amyloid-b 42 (Ab42) fibril

• 超分子: 名称: amyloid-b 42 (Ab42) fibril / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all
• 由来(天然): 生物種: Homo sapiens (ヒト)
• 分子量: 理論値: 4514.10 kDa/nm

分子 #1: Beta-amyloid protein 42

• 分子: 名称: Beta-amyloid protein 42 / タイプ: protein_or_peptide / ID: 1 / コピー数: 8 / 光学異性体: LEVO
• 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 BL21(DE3) (大腸菌)

配列

文字列:

DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IA

UniProtKB: Amyloid-beta precursor protein

実験情報

構造解析

• 手法: クライオ電子顕微鏡法
• 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: 0.34 mg/mL
• 緩衝液: pH: 7.4 / 構成要素 - 濃度: 10.0 mM / 構成要素 - 名称: Sodium Phosphate / 詳細: 10mM Na-phosphate, 0.1% sodium azide
• 凍結: 凍結剤: ETHANE / チャンバー内湿度: 99 % / チャンバー内温度: 93 K / 装置: FEI VITROBOT MARK I; 詳細: Preblot for 12-13 seconds and blot for 2.5-3.0 seconds before plunging.

電子顕微鏡法

• 顕微鏡: FEI TITAN KRIOS
• 撮影: フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k); 検出モード: SUPER-RESOLUTION / デジタル化 - サイズ - 横: 11520 pixel / デジタル化 - サイズ - 縦: 8184 pixel / 撮影したグリッド数: 1 / 実像数: 3383 / 平均露光時間: 1.65 sec. / 平均電子線量: 44.65 e/Ų
• 電子線: 加速電圧: 300 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 FIELD / 最大 デフォーカス（公称値）: 3.0 µm / 最小 デフォーカス（公称値）: 0.5 µm / 倍率（公称値）: 130000
• 試料ステージ: 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER; ホルダー冷却材: NITROGEN
• 実験機器: モデル: Titan Krios / 画像提供: FEI Company

画像解析

• 詳細: Gatan Imaging Filter (GIF) Quantum LS
• 最終 再構成: 想定した対称性 - らせんパラメータ - Δz: 2.46 Å; 想定した対称性 - らせんパラメータ - ΔΦ: -179.09 °; 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: 2.83 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 4.0.0) / 使用した粒子像数: 68481
• Segment selection: 選択した数: 374821 / ソフトウェア - 名称: RELION (ver. 4.0.0)
• 初期モデル: モデルのタイプ: NONE / 詳細: featureless cylinder
• 最終 角度割当: タイプ: NOT APPLICABLE / ソフトウェア - 名称: RELION (ver. 4.0.0); 詳細: 2.46 Angstrom helical rise and -179.09 degree helical twist

原子モデル構築 1

• 詳細: Manually generated model was fit into the density using PHENIX and UCSF Chimera. Further refinements were performed using Xplor-NIH.
• 精密化: プロトコル: OTHER

得られたモデル

PDB-8ezd:
Brain-derived 42-residue amyloid-beta fibril type A