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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: PDB / ID: 8d9s | ||||||||||||
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タイトル | AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on beta-Arf1 | ||||||||||||
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![]() | VIRAL PROTEIN/PROTEIN TRANSPORT / trafficking / AP / HIV / VIRAL PROTEIN-PROTEIN TRANSPORT complex | ||||||||||||
機能・相同性 | ![]() basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / endosome to melanosome transport / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization / melanosome assembly / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I ...basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / endosome to melanosome transport / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization / melanosome assembly / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / Golgi to vacuole transport / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / Golgi Associated Vesicle Biogenesis / symbiont-mediated suppression of host apoptosis / clathrin adaptor activity / suppression by virus of host autophagy / MHC class II antigen presentation / CD4 receptor binding / thioesterase binding / determination of left/right symmetry / clathrin-coated vesicle / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Lysosome Vesicle Biogenesis / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / clathrin binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / Golgi Associated Vesicle Biogenesis / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / MHC class I protein binding / endoplasmic reticulum exit site / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / protein targeting / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / clathrin-coated pit / regulation of calcium-mediated signaling / vesicle-mediated transport / viral life cycle / MHC class II antigen presentation / Neutrophil degranulation / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / kidney development / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle membrane / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / MHC class I peptide loading complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / SH3 domain binding / virion component / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of type II interferon production / peptide antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / Interferon alpha/beta signaling / E3 ubiquitin ligases ubiquitinate target proteins / early endosome membrane / ATPase binding / presynapse / heart development / T cell receptor signaling pathway / antibacterial humoral response / ER-Phagosome pathway / postsynaptic density / early endosome / defense response to Gram-positive bacterium / immune response / Golgi membrane / external side of plasma membrane / lysosomal membrane / intracellular membrane-bounded organelle / innate immune response / signaling receptor binding / GTPase activity / synapse / endoplasmic reticulum membrane / GTP binding / protein kinase binding 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
手法 | 電子顕微鏡法 / サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 20 Å | ||||||||||||
![]() | Hooy, R.M. / Hurley, J.H. | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat. 著者: Richard M Hooy / Yuichiro Iwamoto / Dan A Tudorica / Xuefeng Ren / James H Hurley / ![]() 要旨: The adaptor protein (AP) complexes not only form the inner layer of clathrin coats but also have clathrin-independent roles in membrane traffic whose mechanisms are unknown. HIV-1 Nef hijacks AP-1 to ...The adaptor protein (AP) complexes not only form the inner layer of clathrin coats but also have clathrin-independent roles in membrane traffic whose mechanisms are unknown. HIV-1 Nef hijacks AP-1 to sequester major histocompatibility complex class I (MHC-I), evading immune detection. We found that AP-1:Arf1:Nef:MHC-I forms a coat on tubulated membranes without clathrin and determined its structure. The coat assembles via Arf1 dimer interfaces. AP-1-positive tubules are enriched in cells upon clathrin knockdown. Nef localizes preferentially to AP-1 tubules in cells, explaining how Nef sequesters MHC-I. Coat contact residues are conserved across Arf isoforms and the Arf-dependent AP complexes AP-1, AP-3, and AP-4. Thus, AP complexes can self-assemble with Arf1 into tubular coats without clathrin or other scaffolding factors. The AP-1:Arf1 coat defines the structural basis of a broader class of tubulovesicular membrane coats as an intermediate in clathrin vesicle formation from internal membranes and as an MHC-I sequestration mechanism in HIV-1 infection. | ||||||||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 2.1 MB | 表示 | ![]() |
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PDB形式 | ![]() | 1.2 MB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
関連構造データ | ![]() 27190MC ![]() 7ux3C ![]() 8d4cC ![]() 8d4dC ![]() 8d4eC ![]() 8d4fC ![]() 8d4gC ![]() 8d9rC ![]() 8d9tC ![]() 8d9uC ![]() 8d9vC ![]() 8d9wC C: 同じ文献を引用 ( M: このデータのモデリングに利用したマップデータ |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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要素
-タンパク質 , 2種, 30分子 CHZJX3Ka4Ob5Pc6Qd7NLoepfqgrhsi
#1: タンパク質 | 分子量: 20800.902 Da / 分子数: 18 / 由来タイプ: 組換発現 / 詳細: N-terminal myristoylation at Gly-2 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 24364.404 Da / 分子数: 12 / 由来タイプ: 組換発現 / 詳細: N-terminal myristoylation at Gly-2 由来: (組換発現) ![]() ![]() 遺伝子: nef / 発現宿主: ![]() ![]() |
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-タンパク質・ペプチド , 1種, 6分子 Yyz012
#3: タンパク質・ペプチド | 分子量: 4542.884 Da / 分子数: 6 / Mutation: T345S, S349G, G355S, C363A / 由来タイプ: 組換発現 / 詳細: conjugated to MPB-PE lipid / 由来: (組換発現) ![]() ![]() ![]() |
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-AP-1 complex subunit ... , 4種, 24分子 BADEFIGRTUVWMjklmnStuvwx
#4: タンパク質 | 分子量: 104736.461 Da / 分子数: 6 / Mutation: K359R,E476K / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #5: タンパク質 | 分子量: 68194.094 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() #6: タンパク質 | 分子量: 48606.730 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() #7: タンパク質 | 分子量: 18305.273 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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-非ポリマー , 2種, 36分子 ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#8: 化合物 | ChemComp-GTP / #9: 化合物 | ChemComp-MG / |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: サブトモグラム平均法 |
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試料調製
構成要素 | 名称: AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on beta-Arf1 タイプ: COMPLEX / Entity ID: #1-#7 / 由来: RECOMBINANT |
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分子量 | 実験値: NO |
由来(天然) | 生物種: ![]() |
由来(組換発現) | 生物種: ![]() ![]() |
緩衝液 | pH: 7.2 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: NITROGEN |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 4500 nm / 最小 デフォーカス(公称値): 1500 nm |
撮影 | 電子線照射量: 3 e/Å2 / Avg electron dose per subtomogram: 121 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
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解析
ソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||
3次元再構成 | 解像度: 20 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 2719 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 13 / Num. of volumes extracted: 4208 | ||||||||||||||||||||||||
精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 35.06 Å2 | ||||||||||||||||||||||||
拘束条件 |
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