+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4405 | |||||||||
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タイトル | Helical MyD88 death domain filament | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | helix / filament / TLR / SIGNALING PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 regulation of chemokine (C-X-C motif) ligand 1 production / Toll binding / MyD88 deficiency (TLR5) / regulation of chemokine (C-X-C motif) ligand 2 production / ATP-dependent histone chaperone activity / neutrophil-mediated killing of bacterium / induced systemic resistance / leukocyte activation involved in inflammatory response / TIR domain binding / response to molecule of fungal origin ...regulation of chemokine (C-X-C motif) ligand 1 production / Toll binding / MyD88 deficiency (TLR5) / regulation of chemokine (C-X-C motif) ligand 2 production / ATP-dependent histone chaperone activity / neutrophil-mediated killing of bacterium / induced systemic resistance / leukocyte activation involved in inflammatory response / TIR domain binding / response to molecule of fungal origin / toll-like receptor 8 signaling pathway / positive regulation of lymphocyte proliferation / response to peptidoglycan / positive regulation of interleukin-23 production / establishment of endothelial intestinal barrier / IRAK4 deficiency (TLR5) / regulation of neutrophil migration / cellular response to oxidised low-density lipoprotein particle stimulus / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / Toll-like receptor binding / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / neutrophil activation involved in immune response / interleukin-33-mediated signaling pathway / microglia differentiation / RIP-mediated NFkB activation via ZBP1 / positive regulation of cytokine production involved in inflammatory response / death receptor binding / interleukin-1 receptor binding / MyD88 deficiency (TLR2/4) / positive regulation of macrophage cytokine production / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / skin development / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / 3'-UTR-mediated mRNA stabilization / positive regulation of NLRP3 inflammasome complex assembly / extrinsic component of plasma membrane / immune system process / type I interferon-mediated signaling pathway / defense response to protozoan / response to amine / positive regulation of interleukin-17 production / extrinsic component of cytoplasmic side of plasma membrane / immunoglobulin mediated immune response / positive regulation of type I interferon production / response to amino acid / phagocytosis / signaling adaptor activity / positive regulation of chemokine production / JNK cascade / lipopolysaccharide-mediated signaling pathway / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / response to interleukin-1 / positive regulation of smooth muscle cell proliferation / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / cellular response to mechanical stimulus / response to organic cyclic compound / Interleukin-1 signaling / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / gene expression / ER-Phagosome pathway / cellular response to lipopolysaccharide / response to ethanol / defense response to virus / cell surface receptor signaling pathway / molecular adaptor activity / endosome membrane / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / innate immune response / positive regulation of gene expression / apoptotic process / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / identical protein binding / nucleus / 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: 3.1 Å | |||||||||
データ登録者 | Moncrieffe MC / Bollschweiler D | |||||||||
引用 | ジャーナル: Structure / 年: 2020 タイトル: MyD88 Death-Domain Oligomerization Determines Myddosome Architecture: Implications for Toll-like Receptor Signaling. 著者: Martin C Moncrieffe / Daniel Bollschweiler / Bing Li / Pawel A Penczek / Lee Hopkins / Clare E Bryant / David Klenerman / Nicholas J Gay / 要旨: Toll-like receptors (TLRs) are pivotal in triggering the innate immune response to pathogen infection. Ligand binding induces receptor dimerization which facilitates the recruitment of other post- ...Toll-like receptors (TLRs) are pivotal in triggering the innate immune response to pathogen infection. Ligand binding induces receptor dimerization which facilitates the recruitment of other post-receptor signal transducers into a complex signalosome, the Myddosome. Central to this process is Myeloid differentiation primary response 88 (MyD88), which is required by almost all TLRs, and signaling is thought to proceed via the stepwise, sequential assembly of individual components. Here, we show that the death domains of human MyD88 spontaneously and reversibly associate to form helical filaments in vitro. A 3.1-Å cryoelectron microscopy structure reveals that the architecture of the filament is identical to that of the 6:4 MyD88-IRAK4-IRAK2 hetero-oligomeric Myddosome. Additionally, the death domain of IRAK4 interacts with the filaments to reconstitute the non-stoichiometric 6:4 MyD88-IRAK4 complex. Together, these data suggest that intracellularly, the MyD88 scaffold may be pre-formed and poised for recruitment of IRAKs on receptor activation and TIR engagement. | |||||||||
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_4405.map.gz | 37.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4405-v30.xml emd-4405.xml | 15.7 KB 15.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_4405_fsc.xml | 7.9 KB | 表示 | FSCデータファイル |
画像 | emd_4405.png | 98.2 KB | ||
マスクデータ | emd_4405_msk_1.map | 40.6 MB | マスクマップ | |
Filedesc metadata | emd-4405.cif.gz | 5.7 KB | ||
その他 | emd_4405_half_map_1.map.gz emd_4405_half_map_2.map.gz | 31.2 MB 31.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4405 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4405 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_4405_validation.pdf.gz | 442 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_4405_full_validation.pdf.gz | 441.1 KB | 表示 | |
XML形式データ | emd_4405_validation.xml.gz | 13.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4405 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4405 | 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_4405.map.gz / 形式: CCP4 / 大きさ: 40.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.06 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
-マスク #1
ファイル | emd_4405_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_4405_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_4405_half_map_2.map | ||||||||||||
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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 : Human MyD88
全体 | 名称: Human MyD88 |
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要素 |
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-超分子 #1: Human MyD88
超分子 | 名称: Human MyD88 / 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: Myeloid differentiation primary response protein MyD88
分子 | 名称: Myeloid differentiation primary response protein MyD88 タイプ: protein_or_peptide / ID: 1 / コピー数: 13 / 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: 17.646873 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: SNAMAAGGPG AGSAAPVSST SSLPLAALNM RVRRRLSLFL NVRTQVAADW TALAEEMDFE YLEIRQLETQ ADPTGRLLDA WQGRPGASV GRLLELLTKL GRDDVLLELG PSIEEDCQKY ILKQQQEEAE KPLQVAAVDS SVPRTAELAG ITTLDWSHPQ F EK UniProtKB: Myeloid differentiation primary response protein MyD88 |
-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: 8 構成要素:
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY | |||||||||
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 |
-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 III (4k x 4k) 検出モード: INTEGRATING / 平均電子線量: 0.92 e/Å2 |
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 / 最大 デフォーカス(補正後): 3.2 µm / 最小 デフォーカス(補正後): 0.9 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): 3.1 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 75000 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |