+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-15222 | ||||||||||||
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タイトル | beta-2-microglobulin DeltaN6 amyloid fibril form 2PFa | ||||||||||||
マップデータ | CryoEM helical symmetrised map of b2m-DN6 Form 2PFa (sharpening b-factor of -72) | ||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol 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: 3.0 Å | ||||||||||||
データ登録者 | Wilkinson M / Gallardo R / Radford SE / Ranson NA | ||||||||||||
資金援助 | 英国, 3件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Disease-relevant β-microglobulin variants share a common amyloid fold. 著者: Martin Wilkinson / Rodrigo U Gallardo / Roberto Maya Martinez / Nicolas Guthertz / Masatomo So / Liam D Aubrey / Sheena E Radford / Neil A Ranson / 要旨: β-microglobulin (βm) and its truncated variant ΔΝ6 are co-deposited in amyloid fibrils in the joints, causing the disorder dialysis-related amyloidosis (DRA). Point mutations of βm result in ...β-microglobulin (βm) and its truncated variant ΔΝ6 are co-deposited in amyloid fibrils in the joints, causing the disorder dialysis-related amyloidosis (DRA). Point mutations of βm result in diseases with distinct pathologies. βm-D76N causes a rare systemic amyloidosis with protein deposited in the viscera in the absence of renal failure, whilst βm-V27M is associated with renal failure, with amyloid deposits forming predominantly in the tongue. Here we use cryoEM to determine the structures of fibrils formed from these variants under identical conditions in vitro. We show that each fibril sample is polymorphic, with diversity arising from a 'lego-like' assembly of a common amyloid building block. These results suggest a 'many sequences, one amyloid fold' paradigm in contrast with the recently reported 'one sequence, many amyloid folds' behaviour of intrinsically disordered proteins such as tau and Aβ. | ||||||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_15222.map.gz | 27.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-15222-v30.xml emd-15222.xml | 18 KB 18 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_15222_fsc.xml | 10.7 KB | 表示 | FSCデータファイル |
画像 | emd_15222.png | 86.7 KB | ||
その他 | emd_15222_half_map_1.map.gz emd_15222_half_map_2.map.gz | 94 MB 93.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-15222 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15222 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_15222_validation.pdf.gz | 786.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_15222_full_validation.pdf.gz | 786.2 KB | 表示 | |
XML形式データ | emd_15222_validation.xml.gz | 17.8 KB | 表示 | |
CIF形式データ | emd_15222_validation.cif.gz | 22.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15222 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15222 | 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_15222.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | CryoEM helical symmetrised map of b2m-DN6 Form 2PFa (sharpening b-factor of -72) | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-ハーフマップ: halfmap1
ファイル | emd_15222_half_map_1.map | ||||||||||||
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注釈 | halfmap1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: halfmap2
ファイル | emd_15222_half_map_2.map | ||||||||||||
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注釈 | halfmap2 | ||||||||||||
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 : Amyloid fibril polymorph 2PFa of the beta-2-microglobulin deltaN6...
全体 | 名称: Amyloid fibril polymorph 2PFa of the beta-2-microglobulin deltaN6 variant. |
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要素 |
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-超分子 #1: Amyloid fibril polymorph 2PFa of the beta-2-microglobulin deltaN6...
超分子 | 名称: Amyloid fibril polymorph 2PFa of the beta-2-microglobulin deltaN6 variant. タイプ: complex / ID: 1 / キメラ: Yes / 親要素: 0 / 含まれる分子: all 詳細: Recombinantly expressed and fibrillated in vitro at pH 6.2 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: Beta-2-microglobulin form pI 5.3
分子 | 名称: Beta-2-microglobulin form pI 5.3 / タイプ: protein_or_peptide / ID: 1 詳細: Naturally occuring deltaN6 variant with methionine added prior to peptide sequence to initiate bacterial expression. コピー数: 6 / 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: 11.153478 KDa |
組換発現 | 生物種: Escherichia coli BL21 (大腸菌) |
配列 | 文字列: MIQVYSRHPA ENGKSNFLNC YVSGFHPSDI EVDLLKNGER IEKVEHSDLS FSKDWSFYLL YYTEFTPTEK DEYACRVNHV TLSQPKIVK WDRDM |
-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: 6.2 構成要素:
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グリッド | モデル: EMS Lacey Carbon / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: GRAPHENE OXIDE / 支持フィルム - トポロジー: CONTINUOUS / 前処理 - タイプ: PLASMA CLEANING / 前処理 - 時間: 60 sec. 詳細: The grid was plasma cleaned prior to double addition of Graphene oxide-DDM mixture then used immediately for sample application and vitrification | |||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV / 詳細: 6s blot. | |||||||||
詳細 | Fibrillation conditions: 20 uM monomeric b2m-DN6 at 37C with shaking at 600 rpm for 2-3 weeks |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 撮影したグリッド数: 1 / 実像数: 4095 / 平均露光時間: 7.0 sec. / 平均電子線量: 43.0 e/Å2 詳細: 1687 raw EER frames were collected per image and combined into 40 fractions for processing |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 1.3 µm / 倍率(公称値): 96000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | モデル: Titan Krios / 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 / 温度因子: 53 |
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得られたモデル | PDB-8a7o: |