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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-7455 | |||||||||
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タイトル | Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer | |||||||||
![]() | Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer | |||||||||
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機能・相同性 | ![]() negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex ...negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization / regulation of receptor internalization / Glycosphingolipid transport / response to interferon-alpha / melanosome assembly / regulation of Arp2/3 complex-mediated actin nucleation / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / Intra-Golgi traffic / metalloendopeptidase inhibitor activity / Golgi to vacuole transport / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / Synthesis of PIPs at the Golgi membrane / Golgi Associated Vesicle Biogenesis / clathrin adaptor activity / suppression by virus of host autophagy / MHC class II antigen presentation / positive regulation of leukocyte proliferation / CD4 receptor binding / Nef Mediated CD4 Down-regulation / thioesterase binding / dendritic spine organization / determination of left/right symmetry / long-term synaptic depression / clathrin-coated vesicle / COPI-dependent Golgi-to-ER retrograde traffic / azurophil granule membrane / Lysosome Vesicle Biogenesis / clathrin binding / negative regulation of viral genome replication / Golgi Associated Vesicle Biogenesis / B cell activation / cell leading edge / response to type II interferon / host cell Golgi membrane / MHC class I protein binding / Synthesis of PIPs at the plasma membrane / intracellular copper ion homeostasis / protein targeting / side of membrane / COPI-mediated anterograde transport / clathrin-coated pit / vesicle-mediated transport / regulation of calcium-mediated signaling / viral life cycle / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Neutrophil degranulation / sarcomere / multivesicular body / negative regulation of cell migration / small monomeric GTPase / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / kidney development / virion component / regulation of actin cytoskeleton organization / intracellular protein transport / response to virus / cytoplasmic vesicle membrane / trans-Golgi network / negative regulation of cell growth / cellular response to virus / SH3 domain binding / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / heart development / ATPase binding / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / postsynaptic density / early endosome / neuron projection / membrane raft / apical plasma membrane / protein domain specific binding / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / innate immune response / focal adhesion / signaling receptor binding / GTPase activity / Neutrophil degranulation / GTP binding / protein kinase binding / host cell plasma membrane / perinuclear region of cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
![]() | Morris KL / Buffalo CZ / Hurley JH | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation. 著者: Kyle L Morris / Cosmo Z Buffalo / Christina M Stürzel / Elena Heusinger / Frank Kirchhoff / Xuefeng Ren / James H Hurley / ![]() ![]() 要旨: The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 Å cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, ...The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 Å cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, HIV-1 Nef, and the cytosolic tail of the restriction factor tetherin suggested a mechanism for inactivating tetherin by Golgi retention. The 4.3 Å structure of a mutant Nef-induced dimer of AP-1 showed how the closed trimer is regulated by the dileucine loop of Nef. HDX-MS and mutational analysis were used to show how cargo dynamics leads to alternative Arf1 trimerization, directing Nef targets to be either retained at the trans-Golgi or sorted to lysosomes. Phosphorylation of the NL4-3 M-Nef was shown to regulate AP-1 trimerization, explaining how O-Nefs lacking this phosphosite counteract tetherin but most M-Nefs do not. These observations show how the higher-order organization of a vesicular coat can be allosterically modulated to direct cargoes to distinct fates. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
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マップデータ | ![]() | 201.2 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 12 KB 12 KB | 表示 表示 | ![]() |
画像 | ![]() | 644.4 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 303.4 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 303 KB | 表示 | |
XML形式データ | ![]() | 6.9 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 6dffMC ![]() 7453C ![]() 7454C ![]() 7456C ![]() 7457C ![]() 7458C ![]() 7563C ![]() 6cm9C ![]() 6criC ![]() 6d83C ![]() 6d84C C: 同じ文献を引用 ( M: このマップから作成された原子モデル |
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類似構造データ | |
電子顕微鏡画像生データ | ![]() Data size: 115.4 Data #1: Dose weighted particle stack of AP1:Arf1:tetherin-HIV-Nef [picked particles - multiframe - unprocessed]) ![]() Data size: 34.0 Data #1: Dose weighted particle stack of AP1:Arf1:tetherin-HIV-Nef closed trimer [picked particles - multiframe - unprocessed]) ![]() Data size: 10.1 Data #1: Dose weight particle stack of AP1:Arf1:tetherin-HIV-Nef closed trimer after monomeric subunit extraction using LocalRec [picked particles - multiframe - processed]) |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.067 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
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試料の構成要素
-全体 : Monomer of AP-1:Arf1:Tetherin-Nef
全体 | 名称: Monomer of AP-1:Arf1:Tetherin-Nef |
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要素 |
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-超分子 #1: Monomer of AP-1:Arf1:Tetherin-Nef
超分子 | 名称: Monomer of AP-1:Arf1:Tetherin-Nef / タイプ: complex / ID: 1 / 親要素: 0 |
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由来(天然) | 生物種: ![]() |
組換発現 | 生物種: ![]() ![]() |
分子量 | 理論値: 700 KDa |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.7 mg/mL |
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緩衝液 | pH: 8 詳細: 20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP |
グリッド | モデル: C-flat-1.2/1.3 / 材質: COPPER / メッシュ: 300 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 294 K / 装置: FEI VITROBOT MARK IV |
詳細 | AP-1:Arf1:Tetherin-Nef |
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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) 検出モード: SUPER-RESOLUTION / デジタル化 - サイズ - 横: 3712 pixel / デジタル化 - サイズ - 縦: 3840 pixel / デジタル化 - 画像ごとのフレーム数: 3-38 / 撮影したグリッド数: 1 / 実像数: 2200 / 平均露光時間: 9.5 sec. / 平均電子線量: 62.4 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 50.0 µm / 倍率(補正後): 46849 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.6 mm / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.75 µm / 倍率(公称値): 22500 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |