+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9332 | |||||||||
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タイトル | Helical assembly of the CARD9 CARD | |||||||||
マップデータ | Helical assembly of the CARD9 CARD | |||||||||
試料 |
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キーワード | CARD / filament / helical assembly / death domain / innate immunity / SIGNALING PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 regulation of interleukin-2 production / host-mediated regulation of intestinal microbiota composition / CBM complex / antifungal innate immune response / response to peptidoglycan / positive regulation of stress-activated MAPK cascade / CARD domain binding / positive regulation of innate immune response / positive regulation of cytokine production involved in inflammatory response / neutrophil mediated immunity ...regulation of interleukin-2 production / host-mediated regulation of intestinal microbiota composition / CBM complex / antifungal innate immune response / response to peptidoglycan / positive regulation of stress-activated MAPK cascade / CARD domain binding / positive regulation of innate immune response / positive regulation of cytokine production involved in inflammatory response / neutrophil mediated immunity / positive regulation of T-helper 17 type immune response / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of macrophage cytokine production / response to aldosterone / response to exogenous dsRNA / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-17 production / response to muramyl dipeptide / immunoglobulin mediated immune response / signaling adaptor activity / stress-activated MAPK cascade / positive regulation of chemokine production / JNK cascade / positive regulation of cytokine production / positive regulation of JNK cascade / NOD1/2 Signaling Pathway / protein homooligomerization / CLEC7A (Dectin-1) signaling / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / regulation of apoptotic process / defense response to virus / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / response to xenobiotic stimulus / protein homodimerization activity / protein-containing complex / identical protein binding / metal ion binding / plasma membrane / cytoplasm / 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: 4.0 Å | |||||||||
データ登録者 | Holliday MJ / Rohou A | |||||||||
引用 | ジャーナル: Nat Commun / 年: 2019 タイトル: Structures of autoinhibited and polymerized forms of CARD9 reveal mechanisms of CARD9 and CARD11 activation. 著者: Michael J Holliday / Axel Witt / Alejandro Rodríguez Gama / Benjamin T Walters / Christopher P Arthur / Randal Halfmann / Alexis Rohou / Erin C Dueber / Wayne J Fairbrother / 要旨: CARD9 and CARD11 drive immune cell activation by nucleating Bcl10 polymerization, but are held in an autoinhibited state prior to stimulation. Here, we elucidate the structural basis for this ...CARD9 and CARD11 drive immune cell activation by nucleating Bcl10 polymerization, but are held in an autoinhibited state prior to stimulation. Here, we elucidate the structural basis for this autoinhibition by determining the structure of a region of CARD9 that includes an extensive interface between its caspase recruitment domain (CARD) and coiled-coil domain. We demonstrate, for both CARD9 and CARD11, that disruption of this interface leads to hyperactivation in cells and to the formation of Bcl10-templating filaments in vitro, illuminating the mechanism of action of numerous oncogenic mutations of CARD11. These structural insights enable us to characterize two similar, yet distinct, mechanisms by which autoinhibition is relieved in the course of canonical CARD9 or CARD11 activation. We also dissect the molecular determinants of helical template assembly by solving the structure of the CARD9 filament. Taken together, these findings delineate the structural mechanisms of inhibition and activation within this protein family. | |||||||||
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_9332.map.gz | 30.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9332-v30.xml emd-9332.xml | 18.1 KB 18.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_9332_fsc.xml | 10.4 KB | 表示 | FSCデータファイル |
画像 | emd_9332.png | 101.2 KB | ||
Filedesc metadata | emd-9332.cif.gz | 6.8 KB | ||
その他 | emd_9332_additional.map.gz | 93.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9332 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9332 | 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_9332.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 | Helical assembly of the CARD9 CARD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.085 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
-追加マップ: CARD9 CARD helical filament, sharpened.
ファイル | emd_9332_additional.map | ||||||||||||
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注釈 | CARD9 CARD helical filament, sharpened. | ||||||||||||
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 : Helical assembly of the CARD9 CARD.
全体 | 名称: Helical assembly of the CARD9 CARD. |
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要素 |
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-超分子 #1: Helical assembly of the CARD9 CARD.
超分子 | 名称: Helical assembly of the CARD9 CARD. / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all 詳細: Formed from CARD9 2-152 dimer with an I107E mutation, purified with 1:1 Zn. 1 mM EDTA was added to 0.5 mM protein, followed by 10 minute incubation at 25C. |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 34.0 kDa/nm |
-分子 #1: Caspase recruitment domain-containing protein 9
分子 | 名称: Caspase recruitment domain-containing protein 9 / 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: 17.351873 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: GSDYENDDEC WSVLEGFRVT LTSVIDPSRI TPYLRQCKVL NPDDEEQVLS DPNLVIRKRK VGVLLDILQR TGHKGYVAFL ESLELYYPQ LYKKVTGKEP ARVFSMIEDA SGESGLTQLL MTEVMKLQKK VQDLTALLSS KDDFIKELRV KDS UniProtKB: Caspase recruitment domain-containing protein 9 |
-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
濃度 | 8.67 mg/mL | ||||||||||||||||||
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緩衝液 | pH: 7 構成要素:
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グリッド | モデル: C-flat-2/1 / 材質: COPPER / メッシュ: 200 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. | ||||||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV 詳細: Sample was incubated on the grid for 1 minute, subsequently washed/blotted 6 times in buffer, followed by addition of 3.5 ul buffer, which was blotted by vitrobot for 5 seconds prior to plunging.. | ||||||||||||||||||
詳細 | Formed from CARD9 2-152 dimer with an I107E mutation, purified with 1:1 Zn. 1 mM EDTA was added to 0.5 mM protein, followed by 10 minute incubation at 25C. Sample was subsequently diluted 1:5 before adding to grid. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / デジタル化 - サイズ - 横: 3838 pixel / デジタル化 - サイズ - 縦: 3710 pixel / デジタル化 - 画像ごとのフレーム数: 1-40 / 撮影したグリッド数: 1 / 実像数: 4403 / 平均露光時間: 10.0 sec. / 平均電子線量: 50.9 e/Å2 / 詳細: Collected in movie-mode at 4 frames per second |
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: 100.0 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): 1.25 µm / 倍率(公称値): 130000 |
試料ステージ | 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
-原子モデル構築 1
初期モデル | PDB ID: Chain - Chain ID: A / Chain - Residue range: 8-95 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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詳細 | "Fit in map" in UCSF Chimera was used to fit the previously determined, lowest energy NMR solution structure (PDB ID 6E26) into the sharpened density and to generate 9 symmetry-mates according to the determined helical parameters. The map was then iteratively refined in Phenix and Coot, maintaining strict non-crystallographic symmetry among the CARDs. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
得られたモデル | PDB-6n2p: |