+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8sl0 | ||||||
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タイトル | Structure of a bacterial gasdermin slinky-like oligomer | ||||||
要素 | Gasdermin bGSDM | ||||||
キーワード | IMMUNE SYSTEM / viral mimicry / gasdermin / caspase / autoinhibition / pyroptosis / bats / immunity / cell death | ||||||
機能・相同性 | defense response to virus / plasma membrane / cytoplasm / Gasdermin bGSDM 機能・相同性情報 | ||||||
生物種 | Vitiosangium sp. GDMCC 1.1324 (バクテリア) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.3 Å | ||||||
データ登録者 | Johnson, A.G. / Mayer, M.L. / Kranzusch, P.J. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nature / 年: 2024 タイトル: Structure and assembly of a bacterial gasdermin pore. 著者: Alex G Johnson / Megan L Mayer / Stefan L Schaefer / Nora K McNamara-Bordewick / Gerhard Hummer / Philip J Kranzusch / 要旨: In response to pathogen infection, gasdermin (GSDM) proteins form membrane pores that induce a host cell death process called pyroptosis. Studies of human and mouse GSDM pores have revealed the ...In response to pathogen infection, gasdermin (GSDM) proteins form membrane pores that induce a host cell death process called pyroptosis. Studies of human and mouse GSDM pores have revealed the functions and architectures of assemblies comprising 24 to 33 protomers, but the mechanism and evolutionary origin of membrane targeting and GSDM pore formation remain unknown. Here we determine a structure of a bacterial GSDM (bGSDM) pore and define a conserved mechanism of pore assembly. Engineering a panel of bGSDMs for site-specific proteolytic activation, we demonstrate that diverse bGSDMs form distinct pore sizes that range from smaller mammalian-like assemblies to exceptionally large pores containing more than 50 protomers. We determine a cryo-electron microscopy structure of a Vitiosangium bGSDM in an active 'slinky'-like oligomeric conformation and analyse bGSDM pores in a native lipid environment to create an atomic-level model of a full 52-mer bGSDM pore. Combining our structural analysis with molecular dynamics simulations and cellular assays, our results support a stepwise model of GSDM pore assembly and suggest that a covalently bound palmitoyl can leave a hydrophobic sheath and insert into the membrane before formation of the membrane-spanning β-strand regions. These results reveal the diversity of GSDM pores found in nature and explain the function of an ancient post-translational modification in enabling programmed host cell death. #1: ジャーナル: bioRxiv / 年: 2023 タイトル: Structure and assembly of a bacterial gasdermin pore. 著者: Alex G Johnson / Megan L Mayer / Stefan L Schaefer / Nora K McNamara-Bordewick / Gerhard Hummer / Philip J Kranzusch / 要旨: In response to pathogen infection, gasdermin (GSDM) proteins form membrane pores that induce a host cell death process called pyroptosis. Studies of human and mouse GSDM pores reveal the functions ...In response to pathogen infection, gasdermin (GSDM) proteins form membrane pores that induce a host cell death process called pyroptosis. Studies of human and mouse GSDM pores reveal the functions and architectures of 24-33 protomers assemblies, but the mechanism and evolutionary origin of membrane targeting and GSDM pore formation remain unknown. Here we determine a structure of a bacterial GSDM (bGSDM) pore and define a conserved mechanism of pore assembly. Engineering a panel of bGSDMs for site-specific proteolytic activation, we demonstrate that diverse bGSDMs form distinct pore sizes that range from smaller mammalian-like assemblies to exceptionally large pores containing >50 protomers. We determine a 3.3 Å cryo-EM structure of a bGSDM in an active slinky-like oligomeric conformation and analyze bGSDM pores in a native lipid environment to create an atomic-level model of a full 52-mer bGSDM pore. Combining our structural analysis with molecular dynamics simulations and cellular assays, our results support a stepwise model of GSDM pore assembly and suggest that a covalently bound palmitoyl can leave a hydrophobic sheath and insert into the membrane before formation of the membrane-spanning β-strand regions. These results reveal the diversity of GSDM pores found in nature and explain the function of an ancient post-translational modification in enabling programmed host cell death. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8sl0.cif.gz | 55.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8sl0.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 8sl0.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 8sl0_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8sl0_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | 8sl0_validation.xml.gz | 38.9 KB | 表示 | |
CIF形式データ | 8sl0_validation.cif.gz | 53.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/sl/8sl0 ftp://data.pdbj.org/pub/pdb/validation_reports/sl/8sl0 | HTTPS FTP |
-関連構造データ
関連構造データ | 40570MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 25566.246 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Vitiosangium sp. GDMCC 1.1324 (バクテリア) 遺伝子: DAT35_31115, Ga0334635_1658 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A0A2T4VDM4 |
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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: FILAMENT / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Vitiosangium bGSDM in an active slinky-like oligomeric conformation タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT | ||||||||||||||||||||
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分子量 | 実験値: NO | ||||||||||||||||||||
由来(天然) | 生物種: Vitiosangium sp. GDMCC 1.1324 (バクテリア) | ||||||||||||||||||||
由来(組換発現) | 生物種: Escherichia coli BL21(DE3) (大腸菌) / プラスミド: pET | ||||||||||||||||||||
緩衝液 | pH: 7.5 詳細: 150 mM NaCl, 20 mM HEPES-HOH (pH 7.5), 5.15 mM DDMAB | ||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: The sample was monodisperse | ||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil | ||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277.15 K |
-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: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 700 nm |
撮影 | 電子線照射量: 51.8 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 実像数: 8156 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / 分類: 精密化 | ||||||||||||||||||||||||
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EMソフトウェア | 名称: SerialEM / バージョン: 3.8.6 / カテゴリ: 画像取得 | ||||||||||||||||||||||||
CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 132403 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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