+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3231 | |||||||||
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タイトル | Structure and function based design of Plasmodium-selective proteasome inhibitors | |||||||||
マップデータ | unsharpened and unfiltered 3D reconstruction of the Plasmodium falciparum 20S proteasome core with a ligand | |||||||||
試料 |
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キーワード | proteasome / 20S / Plasmodium / malaria / inhibitor / drug design / cryo-EM | |||||||||
機能・相同性 | 機能・相同性情報 Cross-presentation of soluble exogenous antigens (endosomes) / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / MAPK6/MAPK4 signaling ...Cross-presentation of soluble exogenous antigens (endosomes) / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / MAPK6/MAPK4 signaling / ABC-family proteins mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / Neutrophil degranulation / proteasome core complex / proteasomal ubiquitin-independent protein catabolic process / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / hydrolase activity / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Plasmodium falciparum (マラリア病原虫) / synthetic construct (人工物) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å | |||||||||
データ登録者 | Li H / O' Donoghue AJ / van der Linden WA / Xie SC / Yoo E / Foe IT / Tilley L / Craik CS / da Fonseca PCA / Bogyo M | |||||||||
引用 | ジャーナル: Nature / 年: 2016 タイトル: Structure- and function-based design of Plasmodium-selective proteasome inhibitors. 著者: Hao Li / Anthony J O'Donoghue / Wouter A van der Linden / Stanley C Xie / Euna Yoo / Ian T Foe / Leann Tilley / Charles S Craik / Paula C A da Fonseca / Matthew Bogyo / 要旨: The proteasome is a multi-component protease complex responsible for regulating key processes such as the cell cycle and antigen presentation. Compounds that target the proteasome are potentially ...The proteasome is a multi-component protease complex responsible for regulating key processes such as the cell cycle and antigen presentation. Compounds that target the proteasome are potentially valuable tools for the treatment of pathogens that depend on proteasome function for survival and replication. In particular, proteasome inhibitors have been shown to be toxic for the malaria parasite Plasmodium falciparum at all stages of its life cycle. Most compounds that have been tested against the parasite also inhibit the mammalian proteasome, resulting in toxicity that precludes their use as therapeutic agents. Therefore, better definition of the substrate specificity and structural properties of the Plasmodium proteasome could enable the development of compounds with sufficient selectivity to allow their use as anti-malarial agents. To accomplish this goal, here we use a substrate profiling method to uncover differences in the specificities of the human and P. falciparum proteasome. We design inhibitors based on amino-acid preferences specific to the parasite proteasome, and find that they preferentially inhibit the β2-subunit. We determine the structure of the P. falciparum 20S proteasome bound to the inhibitor using cryo-electron microscopy and single-particle analysis, to a resolution of 3.6 Å. These data reveal the unusually open P. falciparum β2 active site and provide valuable information about active-site architecture that can be used to further refine inhibitor design. Furthermore, consistent with the recent finding that the proteasome is important for stress pathways associated with resistance of artemisinin family anti-malarials, we observe growth inhibition synergism with low doses of this β2-selective inhibitor in artemisinin-sensitive and -resistant parasites. Finally, we demonstrate that a parasite-selective inhibitor could be used to attenuate parasite growth in vivo without appreciable toxicity to the host. Thus, the Plasmodium proteasome is a chemically tractable target that could be exploited by next-generation anti-malarial agents. | |||||||||
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_3231.map.gz | 58.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3231-v30.xml emd-3231.xml | 10.4 KB 10.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_3231.jpg | 191.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3231 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3231 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_3231_validation.pdf.gz | 316 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_3231_full_validation.pdf.gz | 315.1 KB | 表示 | |
XML形式データ | emd_3231_validation.xml.gz | 6.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3231 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3231 | 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_3231.map.gz / 形式: CCP4 / 大きさ: 62.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | unsharpened and unfiltered 3D reconstruction of the Plasmodium falciparum 20S proteasome core with a ligand | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.04 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 : Plasmodium falciparum 20S proteasome core bound to a specific inh...
全体 | 名称: Plasmodium falciparum 20S proteasome core bound to a specific inhibitor |
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要素 |
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-超分子 #1000: Plasmodium falciparum 20S proteasome core bound to a specific inh...
超分子 | 名称: Plasmodium falciparum 20S proteasome core bound to a specific inhibitor タイプ: sample / ID: 1000 / Number unique components: 2 |
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分子量 | 理論値: 760 KDa |
-分子 #1: proteasome 20S core
分子 | 名称: proteasome 20S core / タイプ: protein_or_peptide / ID: 1 詳細: The sample protein components are deposited in the PlasmoDB (the Plasmodium genome resource) 集合状態: dimer / 組換発現: No |
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由来(天然) | 生物種: Plasmodium falciparum (マラリア病原虫) |
分子量 | 理論値: 760 KDa |
-分子 #2: Mor-WLW vinyl sulphone (HET: 7F1)
分子 | 名称: Mor-WLW vinyl sulphone (HET: 7F1) / タイプ: ligand / ID: 2 / 組換発現: No |
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由来(天然) | 生物種: synthetic construct (人工物) |
-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 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.1 mg/mL |
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緩衝液 | pH: 7.5 / 詳細: 50mM Tris HCl, 5mM MgCl2, 1mM dithiotreitol |
グリッド | 詳細: 1.2/1.3 Quantifoil, 300 mesh Cu grids, coated with freshly floated thin layer of carbon |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / 装置: FEI VITROBOT MARK III / 手法: blot 2.5 seconds before plunging |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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詳細 | Each exposure was recorded as 17 individual frames captured at a rate of 0.056 second/frame, each with an electron dose of 2.8 electrons/square angstrom. Data-set recorded using EPU software. |
日付 | 2014年9月3日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 実像数: 1816 / 平均電子線量: 48 e/Å2 / 詳細: each image was recorded as 17 frames |
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): 3.2 µm / 最小 デフォーカス(公称値): 1.6 µm / 倍率(公称値): 75000 |
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
詳細 | The particles were selected automatically using Relion, followed by manual inspection for the removal of false positives and addition of false negatives |
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CTF補正 | 詳細: full recorded image |
最終 再構成 | 想定した対称性 - 点群: C2 (2回回転対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 3.6 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Tigris, Spider, Imagic / 使用した粒子像数: 97720 |
-原子モデル構築 1
初期モデル | PDB ID: |
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詳細 | The initial models of the Plasmodium falciparum 20S proteasome core subunits were obtained using the PHYRE 2 structure prediction server; model building was done using real space refinement in Coot and Phenix |
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
得られたモデル | PDB-5fmg: |