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基本情報
登録情報 | データベース: EMDB / ID: EMD-2805 | |||||||||
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タイトル | Refined negative stain electron microscopy reconstruction of the tip complex from the type III secretion system of Shigella flexneri with MxiH mutation Q51A | |||||||||
![]() | Reconstruction of the tip complex and needle from the type III secretion system of Shigella flexneri with MxiH mutation Q51A and using groups of individual images | |||||||||
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![]() | Tip complex / Type III secretion system / Shigella flexneri / Refined Q51A | |||||||||
生物種 | ![]() | |||||||||
手法 | 単粒子再構成法 / ネガティブ染色法 / 解像度: 19.0 Å | |||||||||
![]() | Cheung M / Shen D / Makino F / Kato T / Roehrich D / Martinez-Argudo I / Walker ML / Murillo I / Liu X / Pain M ...Cheung M / Shen D / Makino F / Kato T / Roehrich D / Martinez-Argudo I / Walker ML / Murillo I / Liu X / Pain M / Brown J / Frazer G / Mantell J / Mina P / Todd T / Sessions RB / Namba K / Blocker AJ | |||||||||
![]() | ジャーナル: Proc Natl Acad Sci U S A / 年: 2008 タイトル: What's the point of the type III secretion system needle? 著者: Ariel J Blocker / Janet E Deane / Andreas K J Veenendaal / Pietro Roversi / Julie L Hodgkinson / Steven Johnson / Susan M Lea / ![]() 要旨: Recent work by several groups has significantly expanded our knowledge of the structure, regulation of assembly, and function of components of the extracellular portion of the type III secretion ...Recent work by several groups has significantly expanded our knowledge of the structure, regulation of assembly, and function of components of the extracellular portion of the type III secretion system (T3SS) of Gram-negative bacteria. This perspective presents a structure-informed analysis of functional data and discusses three nonmutually exclusive models of how a key aspect of T3SS biology, the sensing of host cells, may be performed. | |||||||||
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: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 19.7 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 16.3 KB 16.3 KB | 表示 表示 | ![]() |
画像 | ![]() | 48.3 KB | ||
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文書・要旨 | ![]() | 216.3 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 215.4 KB | 表示 | |
XML形式データ | ![]() | 6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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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 | Reconstruction of the tip complex and needle from the type III secretion system of Shigella flexneri with MxiH mutation Q51A and using groups of individual images | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.12 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 : Conformation of the tip complex from the type III secretion syste...
全体 | 名称: Conformation of the tip complex from the type III secretion system of Shigella flexneri bound to the needle with MxiH mutation Q51A |
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要素 |
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-超分子 #1000: Conformation of the tip complex from the type III secretion syste...
超分子 | 名称: Conformation of the tip complex from the type III secretion system of Shigella flexneri bound to the needle with MxiH mutation Q51A タイプ: sample / ID: 1000 詳細: Tip complexes were analysed from purified needle complexes and therefore when still bound to the needle tip 集合状態: Five subunits of the tip complex bound to fifty subunits of the needle Number unique components: 2 |
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分子量 | 理論値: 680 KDa |
-超分子 #1: Tip complex and needle
超分子 | 名称: Tip complex and needle / タイプ: organelle_or_cellular_component / ID: 1 / コピー数: 1 / 集合状態: Heteropentameric / 組換発現: Yes |
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Ref GO | divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp ... divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp kGO3A00302 57ampajax1 classpoptr giGO003025 7ispandiv |
Ref INTERPRO | divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp ... divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp kIPR006135 ampajax1cl asspoptrgi IPR006135i spandiv |
由来(天然) | 生物種: ![]() 細胞中の位置: Extracellular component of membrane embedded complex |
分子量 | 理論値: 210 KDa |
組換発現 | 生物種: ![]() |
-超分子 #2: Tip complex and needle
超分子 | 名称: Tip complex and needle / タイプ: organelle_or_cellular_component / ID: 2 / コピー数: 1 / 組換発現: Yes |
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Ref GO | divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp ... divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp kGO3A00302 57ampajax1 classpoptr giGO003025 7ispandiv |
Ref INTERPRO | divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp ... divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp kIPR006135 ampajax1cl asspoptrgi IPR006135i spandiv |
由来(天然) | 生物種: ![]() 細胞中の位置: Extracellular component of membrane embedded complex |
分子量 | 理論値: 470 KDa |
組換発現 | 生物種: ![]() |
-実験情報
-構造解析
手法 | ネガティブ染色法 |
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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
濃度 | 0.1 mg/mL |
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緩衝液 | pH: 8 詳細: 0.1% (w/v) DDM, 150 mM NaCl, 25 mM Tris pH 8, 5 mM EDTA |
染色 | タイプ: NEGATIVE 詳細: Carbon coating mica sheets were submerged in a drop of 0.01% (w/v) DDM until the carbon sheet partially detached from the mica. The mica was then submerged in the sample for 5 s, then ...詳細: Carbon coating mica sheets were submerged in a drop of 0.01% (w/v) DDM until the carbon sheet partially detached from the mica. The mica was then submerged in the sample for 5 s, then submerged in a drop of water for 5 s. The mica was then placed onto the surface of a drop of 1% uranyl acetate and allowed to sink, causing the carbon to float on the surface of the drop. After 10 s, the carbon sheet was adsorbed onto a grid. |
グリッド | 詳細: 300 mesh copper grid with a thin carbon film to which the specimen was adsorbed to |
凍結 | 凍結剤: NONE / 装置: OTHER |
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電子顕微鏡法
顕微鏡 | FEI TECNAI 20 |
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アライメント法 | Legacy - 非点収差: Thon rings visualised at 50-100,000 times magnification using the fast FT and corrected accordingly Legacy - Electron beam tilt params: 0 |
日付 | 2011年8月31日 |
撮影 | カテゴリ: CCD / フィルム・検出器のモデル: FEI EAGLE (4k x 4k) / デジタル化 - サンプリング間隔: 15 µm / 実像数: 250 / 平均電子線量: 9 e/Å2 / カメラ長: 460 / Od range: 3.56 / ビット/ピクセル: 16 |
電子線 | 加速電圧: 200 kV / 電子線源: LAB6 |
電子光学系 | 倍率(補正後): 70754 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2 mm / 最大 デフォーカス(公称値): 1.4 µm / 最小 デフォーカス(公称値): 1.4 µm / 倍率(公称値): 50000 |
試料ステージ | 試料ホルダー: FEI single tilt holder / 試料ホルダーモデル: SIDE ENTRY, EUCENTRIC |
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画像解析
詳細 | Particles were selected using helix boxer from EMAN2. After alignment, Euler angles were determined by projection matching with projections of a map Q51A. The reconstruction was iterated and helical pattern searching and imposition was applied to each new reference generated after each iteration. |
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CTF補正 | 詳細: First zero set to 18 angstrom, no CTF correction not required |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 19.0 Å / 解像度の算出法: OTHER ソフトウェア - 名称: EMAN2, SPIDER, bespoke-2D-alignment, bespoke-X-and-Y-shifting 使用した粒子像数: 2545 |
最終 角度割当 | 詳細: SPIDER: theta 4 degrees |