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基本情報
登録情報 | データベース: PDB / ID: 4d3e | ||||||
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タイトル | Tetramer of IpaD, modified from 2J0O, fitted into negative stain electron microscopy reconstruction of the wild type tip complex from the type III secretion system of Shigella flexneri | ||||||
![]() | INVASIN IPAD | ||||||
![]() | CELL INVASION / TIP COMPLEX / TYPE III SECRETION SYSTEM / SHIGELLA FLEXNERI / WILD TYPE / IPAD | ||||||
機能・相同性 | ![]() | ||||||
生物種 | ![]() | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / ネガティブ染色法 / 解像度: 24 Å | ||||||
![]() | Cheung, M. / Shen, D.-K. / Makino, F. / Kato, T. / Roehrich, D. / Martinez-Argudo, I. / Walker, M.L. / Murillo, I. / Liu, X. / Pain, M. ...Cheung, M. / Shen, D.-K. / Makino, F. / Kato, T. / Roehrich, D. / Martinez-Argudo, I. / Walker, M.L. / Murillo, I. / Liu, X. / Pain, M. / Brown, J. / Frazer, G. / Mantell, J. / Mina, P. / Todd, T. / Sessions, R.B. / Namba, K. / Blocker, A.J. | ||||||
![]() | ![]() タイトル: Three-dimensional electron microscopy reconstruction and cysteine-mediated crosslinking provide a model of the type III secretion system needle tip complex. 著者: Martin Cheung / Da-Kang Shen / Fumiaki Makino / Takayuki Kato / A Dorothea Roehrich / Isabel Martinez-Argudo / Matthew L Walker / Isabel Murillo / Xia Liu / Maria Pain / James Brown / Gordon ...著者: Martin Cheung / Da-Kang Shen / Fumiaki Makino / Takayuki Kato / A Dorothea Roehrich / Isabel Martinez-Argudo / Matthew L Walker / Isabel Murillo / Xia Liu / Maria Pain / James Brown / Gordon Frazer / Judith Mantell / Petros Mina / Thomas Todd / Richard B Sessions / Keiichi Namba / Ariel J Blocker / ![]() 要旨: Type III secretion systems are found in many Gram-negative bacteria. They are activated by contact with eukaryotic cells and inject virulence proteins inside them. Host cell detection requires a ...Type III secretion systems are found in many Gram-negative bacteria. They are activated by contact with eukaryotic cells and inject virulence proteins inside them. Host cell detection requires a protein complex located at the tip of the device's external injection needle. The Shigella tip complex (TC) is composed of IpaD, a hydrophilic protein, and IpaB, a hydrophobic protein, which later forms part of the injection pore in the host membrane. Here we used labelling and crosslinking methods to show that TCs from a ΔipaB strain contain five IpaD subunits while the TCs from wild-type can also contain one IpaB and four IpaD subunits. Electron microscopy followed by single particle and helical image analysis was used to reconstruct three-dimensional images of TCs at ∼ 20 Å resolution. Docking of an IpaD crystal structure, constrained by the crosslinks observed, reveals that TC organisation is different from that of all previously proposed models. Our findings suggest new mechanisms for TC assembly and function. The TC is the only site within these secretion systems targeted by disease-protecting antibodies. By suggesting how these act, our work will allow improvement of prophylactic and therapeutic strategies. #1: ![]() タイトル: Self-chaperoning of the type III secretion system needle tip proteins IpaD and BipD. 著者: Steven Johnson / Pietro Roversi / Marianela Espina / Andrew Olive / Janet E Deane / Susan Birket / Terry Field / William D Picking / Ariel J Blocker / Edouard E Galyov / Wendy L Picking / Susan M Lea / ![]() 要旨: Bacteria expressing type III secretion systems (T3SS) have been responsible for the deaths of millions worldwide, acting as key virulence elements in diseases ranging from plague to typhoid fever. ...Bacteria expressing type III secretion systems (T3SS) have been responsible for the deaths of millions worldwide, acting as key virulence elements in diseases ranging from plague to typhoid fever. The T3SS is composed of a basal body, which traverses both bacterial membranes, and an external needle through which effector proteins are secreted. We report multiple crystal structures of two proteins that sit at the tip of the needle and are essential for virulence: IpaD from Shigella flexneri and BipD from Burkholderia pseudomallei. The structures reveal that the N-terminal domains of the molecules are intramolecular chaperones that prevent premature oligomerization, as well as sharing structural homology with proteins involved in eukaryotic actin rearrangement. Crystal packing has allowed us to construct a model for the tip complex that is supported by mutations designed using the structure. | ||||||
履歴 |
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構造の表示
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 160.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 131.9 KB | 表示 | ![]() |
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アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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モデル数 | 4 |
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要素
#1: タンパク質 | 分子量: 23076.775 Da / 分子数: 1 断片: COILDED-COIL AND GLOBULAR DOMAIN, UNP RESIDUES 125-332 由来タイプ: 組換発現 詳細: YES [LACKING FIRST 124 AA AND WITH LAST 10 AA MODELLED INTO HELIX] 由来: (組換発現) ![]() 発現宿主: ![]() ![]() |
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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: 単粒子再構成法 |
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試料調製
構成要素 | 名称: WILD-TYPE T3SS NEEDLE COMPLEX / タイプ: COMPLEX / 詳細: FIRST ZERO OF CTF SET TO 19A FOR ALL MICROGRAPHS |
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緩衝液 | 名称: 0.1% (W/V) DDM, 150 MM NACL, 25 MM TRIS PH 8, 5 MM EDTA pH: 8 詳細: 0.1% (W/V) DDM, 150 MM NACL, 25 MM TRIS PH 8, 5 MM EDTA |
試料 | 濃度: 0.1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: YES / 凍結: NO |
染色 | タイプ: NEGATIVE / 染色剤: uranyl acetate |
試料支持 | 詳細: CARBON |
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電子顕微鏡撮影
顕微鏡 | モデル: FEI TECNAI 20 / 日付: 2011年8月31日 |
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電子銃 | 電子線源: LAB6 / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 50000 X / 倍率(補正後): 70754 X / 最大 デフォーカス(公称値): 1600 nm / 最小 デフォーカス(公称値): 1200 nm / Cs: 2 mm |
撮影 | 電子線照射量: 90 e/Å2 / フィルム・検出器のモデル: FEI EAGLE (4k x 4k) |
画像スキャン | デジタル画像の数: 300 |
放射波長 | 相対比: 1 |
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解析
EMソフトウェア |
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対称性 | 点対称性: C1 (非対称) | ||||||||||||||||
3次元再構成 | 手法: MIX OF SINGLE PARTICLE AND HELICAL RECONSTRUCTION METHODS 解像度: 24 Å / 粒子像の数: 2963 / ピクセルサイズ(実測値): 2.12 Å 詳細: THIS MODEL IS RESULT OF RIGID-BODY TRANSFORMATION OF AN EXISTING PDB MODEL, CONSTRAINED BY A 24 A RESOLUTION EM MAP AND SOME CYSTEINE-MEDIATED CROSSLINKING DATA. THEREFORE, IT DOES NOT ...詳細: THIS MODEL IS RESULT OF RIGID-BODY TRANSFORMATION OF AN EXISTING PDB MODEL, CONSTRAINED BY A 24 A RESOLUTION EM MAP AND SOME CYSTEINE-MEDIATED CROSSLINKING DATA. THEREFORE, IT DOES NOT SUPPORT ATOMISTIC INTERPRETATIONS BECAUSE OF LACK OF RESOLUTION. 対称性のタイプ: POINT | ||||||||||||||||
原子モデル構築 | プロトコル: OTHER / 空間: REAL / 詳細: METHOD--SEE PUBLICATION REFINEMENT PROTOCOL--X-RAY | ||||||||||||||||
原子モデル構築 | PDB-ID: 2J0O Accession code: 2J0O / Source name: PDB / タイプ: experimental model | ||||||||||||||||
精密化 | 最高解像度: 24 Å | ||||||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 2.12 Å
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