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基本情報
登録情報 | データベース: EMDB / ID: EMD-20024 | ||||||||||||||||||||||||
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タイトル | Cryo-EM structure of Helicobacter pylori VacA hexamer | ||||||||||||||||||||||||
![]() | Cryo-EM structure of Helicobacter pylori VacA hexamer | ||||||||||||||||||||||||
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機能・相同性 | ![]() cell outer membrane / toxin activity / periplasmic space / cell surface / extracellular region 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: 3.8 Å | ||||||||||||||||||||||||
![]() | Erwin AL / Cover TL / Ohi MD | ||||||||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Cryo-EM Analysis Reveals Structural Basis of Helicobacter pylori VacA Toxin Oligomerization. 著者: Min Su / Amanda L Erwin / Anne M Campbell / Tasia M Pyburn / Lauren E Salay / Jessica L Hanks / D Borden Lacy / David L Akey / Timothy L Cover / Melanie D Ohi / ![]() 要旨: Helicobacter pylori colonizes the human stomach and contributes to the development of gastric cancer and peptic ulcer disease. H. pylori secretes a pore-forming toxin called vacuolating cytotoxin A ...Helicobacter pylori colonizes the human stomach and contributes to the development of gastric cancer and peptic ulcer disease. H. pylori secretes a pore-forming toxin called vacuolating cytotoxin A (VacA), which contains two domains (p33 and p55) and assembles into oligomeric structures. Using single-particle cryo-electron microscopy, we have determined low-resolution structures of a VacA dodecamer and heptamer, as well as a 3.8-Å structure of the VacA hexamer. These analyses show that VacA p88 consists predominantly of a right-handed beta-helix that extends from the p55 domain into the p33 domain. We map the regions of p33 and p55 involved in hexamer assembly, model how interactions between protomers support heptamer formation, and identify surfaces of VacA that likely contact membrane. This work provides structural insights into the process of VacA oligomerization and identifies regions of VacA protomers that are predicted to contact the host cell surface during channel formation. | ||||||||||||||||||||||||
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: ![]() ![]() ![]() |
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マップデータ | ![]() | 115.9 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 12.6 KB 12.6 KB | 表示 表示 | ![]() |
画像 | ![]() | 37.5 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 620.3 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 619.8 KB | 表示 | |
XML形式データ | ![]() | 5.9 KB | 表示 | |
CIF形式データ | ![]() | 6.8 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM structure of Helicobacter pylori VacA hexamer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.25 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
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試料の構成要素
-全体 : Vacuolating cytotoxin A
全体 | 名称: Vacuolating cytotoxin A |
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要素 |
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-超分子 #1: Vacuolating cytotoxin A
超分子 | 名称: Vacuolating cytotoxin A / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all / 詳細: Hexamer |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 実験値: 528 KDa |
-分子 #1: Vacuolating cytotoxin autotransporter
分子 | 名称: Vacuolating cytotoxin autotransporter / タイプ: protein_or_peptide / ID: 1 / コピー数: 6 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 70.392578 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)QPTQVID GPFAGGKDTV VNIDRINTKA DGTIKVGGFK ASLTTNAAHL NIGKGGVN L SNQASGRTLL VENLTGNITV DGPLRVNNQV GGYALAGSSA NFEFKAGVDT KNGTATFNND ISLGRFVNLK VDAHTANFK GIDTGNGGFN TLDFSGVTNK VNINKLITAS TNVAVKNFNI NELIVKTNGV SVGEYTHFSE DIGSQSRINT VRLETGTRSI FSGGVKFKS GEKLVIDEFY YSPWNYFDAR NIKNVEITRK FASSTPENPW GTSKLMFNNL TLGQNAVMDY SQFSNLTIQG D FINNQGTI NYLVRGGKVA TLNVGNAAAM MFNNDIDSAT GFYKPLIKIN SAQDLIKNTE HVLLKAKIIG YGNVSTGTNG IS NVNLEEQ FKERLALYNN NNRMDTCVVR NTDDIKACGM AIGNQSMVNN PDNYKYLIGK AWKNIGISKT ANGSKISVYY LGN STPTEN GGNTTNLPTN T |
-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
緩衝液 | pH: 8 |
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グリッド | 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
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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) 平均電子線量: 48.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
初期モデル | モデルのタイプ: OTHER / 詳細: Ab initio model |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 133827 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: PROJECTION MATCHING |