+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-20900 | |||||||||
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タイトル | human prion protein fibril, M129 variant | |||||||||
マップデータ | Human prion protein fibril, M129 variant | |||||||||
試料 |
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キーワード | amyloid / fibril / prion / filament / protein fibril / fiber / PrP | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of glutamate receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions ...positive regulation of glutamate receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions / negative regulation of interleukin-17 production / regulation of potassium ion transmembrane transport / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade / extrinsic component of membrane / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of interleukin-2 production / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / cuprous ion binding / response to amyloid-beta / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / long-term memory / response to cadmium ion / regulation of peptidyl-tyrosine phosphorylation / inclusion body / cellular response to copper ion / neuron projection maintenance / positive regulation of calcium-mediated signaling / tubulin binding / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / positive regulation of neuron apoptotic process / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / cellular response to xenobiotic stimulus / protein-folding chaperone binding / signaling receptor activity / amyloid-beta binding / microtubule binding / protease binding / nuclear membrane / transmembrane transporter binding / response to oxidative stress / postsynapse / molecular adaptor activity / postsynaptic density / learning or memory / regulation of cell cycle / membrane raft / copper ion binding / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm 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: 3.5 Å | |||||||||
データ登録者 | Glynn C / Sawaya MR | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2020 タイトル: Cryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant core. 著者: Calina Glynn / Michael R Sawaya / Peng Ge / Marcus Gallagher-Jones / Connor W Short / Ronquiajah Bowman / Marcin Apostol / Z Hong Zhou / David S Eisenberg / Jose A Rodriguez / 要旨: Self-templating assemblies of the human prion protein are clinically associated with transmissible spongiform encephalopathies. Here we present the cryo-EM structure of a denaturant- and protease- ...Self-templating assemblies of the human prion protein are clinically associated with transmissible spongiform encephalopathies. Here we present the cryo-EM structure of a denaturant- and protease-resistant fibril formed in vitro spontaneously by a 9.7-kDa unglycosylated fragment of the human prion protein. This human prion fibril contains two protofilaments intertwined with screw symmetry and linked by a tightly packed hydrophobic interface. Each protofilament consists of an extended beta arch formed by residues 106 to 145 of the prion protein, a hydrophobic and highly fibrillogenic disease-associated segment. Such structures of prion polymorphs serve as blueprints on which to evaluate the potential impact of sequence variants on prion disease. | |||||||||
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_20900.map.gz | 171.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-20900-v30.xml emd-20900.xml | 9.5 KB 9.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_20900.png | 79.2 KB | ||
Filedesc metadata | emd-20900.cif.gz | 5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-20900 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20900 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_20900_validation.pdf.gz | 362.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_20900_full_validation.pdf.gz | 362.2 KB | 表示 | |
XML形式データ | emd_20900_validation.xml.gz | 7.5 KB | 表示 | |
CIF形式データ | emd_20900_validation.cif.gz | 8.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20900 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20900 | 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_20900.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Human prion protein fibril, M129 variant | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.07 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 : Fiber of human prion protein
全体 | 名称: Fiber of human prion protein |
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要素 |
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-超分子 #1: Fiber of human prion protein
超分子 | 名称: Fiber of human prion protein / 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) |
-分子 #1: Major prion protein
分子 | 名称: Major prion protein / タイプ: protein_or_peptide / ID: 1 / コピー数: 10 / 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: 9.685771 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: GTHSQWNKPS KPKTNMKHMA GAAAAGAVVG GLGGYMLGSA MSRPIIHFGS DYEDRYYREN MHRYPNQVYY RPMDEYSNQN NFVHD UniProtKB: Major prion protein |
-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: 4 |
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グリッド | 詳細: unspecified |
凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK IV |
-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: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 1.2 e/Å2 |
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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 想定した対称性 - らせんパラメータ - Δz: 2.4 Å 想定した対称性 - らせんパラメータ - ΔΦ: 179.3 ° 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: 3.5 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: RELION / 使用した粒子像数: 76246 |
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初期モデル | モデルのタイプ: NONE / 詳細: Gaussian cylinder |
最終 角度割当 | タイプ: NOT APPLICABLE |