+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0634 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Helicobacter pylori Cag T4SS innermembrane complex | |||||||||
マップデータ | Cag T4SS innermembrane complex | |||||||||
試料 |
| |||||||||
生物種 | Helicobacter pylori (ピロリ菌) | |||||||||
手法 | サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 47.8 Å | |||||||||
データ登録者 | Hu B / Christie PJ | |||||||||
引用 | ジャーナル: mBio / 年: 2019 タイトル: Molecular Architecture of the Helicobacter pylori Cag Type IV Secretion System. 著者: Bo Hu / Pratick Khara / Liqiang Song / Aung Soe Lin / Arwen E Frick-Cheng / M Lorena Harvey / Timothy L Cover / Peter J Christie / 要旨: colonizes about half of humans worldwide, and its presence in the gastric mucosa is associated with an increased risk of gastric adenocarcinoma, gastric lymphoma, and peptic ulcer disease. strains ... colonizes about half of humans worldwide, and its presence in the gastric mucosa is associated with an increased risk of gastric adenocarcinoma, gastric lymphoma, and peptic ulcer disease. strains carrying the pathogenicity island (PAI) are associated with increased risk of disease progression. The PAI encodes the Cag type IV secretion system (Cag), which delivers the CagA oncoprotein and other effector molecules into human gastric epithelial cells. We visualized structures of native and mutant Cag machines on the cell envelope by cryoelectron tomography. Individual cells contain multiple Cag nanomachines, each composed of a wheel-shaped outer membrane complex (OMC) with 14-fold symmetry and an inner membrane complex (IMC) with 6-fold symmetry. CagX, CagY, and CagM are required for assembly of the OMC, whereas strains lacking Cag3 and CagT produce outer membrane complexes lacking peripheral components. The IMC, which has never been visualized in detail, is configured as six tiers in cross-section view and three concentric rings surrounding a central channel in end-on view. The IMC contains three T4SS ATPases: (i) VirB4-like CagE, arranged as a hexamer of dimers at the channel entrance; (ii) a hexamer of VirB11-like Cagα, docked at the base of the CagE hexamer; and (iii) VirD4-like Cagβ and other unspecified Cag subunits, associated with the stacked CagE/Cagα complex and forming the outermost rings. The Cag and recently solved Dot/Icm system comprise new structural prototypes for the T4SS superfamily. Bacterial type IV secretion systems (T4SSs) have been phylogenetically grouped into two subfamilies. The T4ASSs, represented by the VirB/VirD4, include "minimized" machines assembled from 12 VirB- and VirD4-like subunits and compositionally larger systems such as the Cag T4BSSs encompass systems closely related in subunit composition to the Dot/Icm Here, we present structures of native and mutant Cag machines determined by cryoelectron tomography. We identify distinct outer and inner membrane complexes and, for the first time, visualize structural contributions of all three "signature" ATPases of T4SSs at the cytoplasmic entrance of the translocation channel. Despite their evolutionary divergence, the Cag aligns structurally much more closely to the Dot/Icm than an available VirB/VirD4 subcomplex. Our findings highlight the diversity of T4SSs and suggest a structural classification scheme in which T4SSs are grouped as minimized VirB/VirD4-like or larger Cag-like and Dot/Icm-like systems. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_0634.map.gz | 1.4 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-0634-v30.xml emd-0634.xml | 7.3 KB 7.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0634.png | 145.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0634 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0634 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0634_validation.pdf.gz | 78.6 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_0634_full_validation.pdf.gz | 77.7 KB | 表示 | |
XML形式データ | emd_0634_validation.xml.gz | 494 B | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0634 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0634 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|
-マップ
ファイル | ダウンロード / ファイル: emd_0634.map.gz / 形式: CCP4 / 大きさ: 2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Cag T4SS innermembrane complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
-全体 : Cag T4SS
全体 | 名称: Cag T4SS |
---|---|
要素 |
|
-超分子 #1: Cag T4SS
超分子 | 名称: Cag T4SS / タイプ: cell / ID: 1 / 親要素: 0 |
---|---|
由来(天然) | 生物種: Helicobacter pylori (ピロリ菌) |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
解析 | サブトモグラム平均法 |
試料の集合状態 | cell |
-試料調製
緩衝液 | pH: 7 |
---|---|
グリッド | 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI POLARA 300 |
---|---|
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均電子線量: 1.8 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: OTHER / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
-画像解析
最終 再構成 | 想定した対称性 - 点群: C6 (6回回転対称) / 解像度のタイプ: BY AUTHOR / 解像度: 47.8 Å / 解像度の算出法: FSC 0.5 CUT-OFF / 使用したサブトモグラム数: 1280 |
---|---|
抽出 | トモグラム数: 425 / 使用した粒子像数: 1280 |
最終 角度割当 | タイプ: OTHER |