+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3234 | |||||||||
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タイトル | Representative tomogram as used in: Structure of bacterial chemotaxis signaling CheA2-trimer core complex by cryo-electron tomography and subvolume averaging | |||||||||
マップデータ | The tomogram is is binned by 4 while those used in the corresponding subTomogram work were used at full sampling. The protein array is best viewed by rotating around the X-axis 3.3 degrees, and the Y-axis 0.3 degrees as Imod Slicer angles. | |||||||||
試料 |
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キーワード | Bacterial chemotaxis / Signal transduction / cryo-Electron Tomography / Molecular dynamics simulation / all-atom | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of protein modification process / detection of chemical stimulus / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / protein histidine kinase binding / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / cell tip / protein histidine kinase activity ...negative regulation of protein modification process / detection of chemical stimulus / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / protein histidine kinase binding / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / cell tip / protein histidine kinase activity / regulation of chemotaxis / thermotaxis / signal complex assembly / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / establishment of localization in cell / cellular response to amino acid stimulus / protein homooligomerization / transmembrane signaling receptor activity / chemotaxis / protein domain specific binding / signal transduction / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli (大腸菌) | |||||||||
手法 | 電子線トモグラフィー法 / クライオ電子顕微鏡法 | |||||||||
データ登録者 | Cassidy CK / Himes BA / Alvarez FJ / Ma J / Zhou G / Perilla JR / Schulten K / Zhang P | |||||||||
引用 | ジャーナル: Elife / 年: 2015 タイトル: CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling. 著者: C Keith Cassidy / Benjamin A Himes / Frances J Alvarez / Jun Ma / Gongpu Zhao / Juan R Perilla / Klaus Schulten / Peijun Zhang / 要旨: Chemotactic responses in bacteria require large, highly ordered arrays of sensory proteins to mediate the signal transduction that ultimately controls cell motility. A mechanistic understanding of ...Chemotactic responses in bacteria require large, highly ordered arrays of sensory proteins to mediate the signal transduction that ultimately controls cell motility. A mechanistic understanding of the molecular events underlying signaling, however, has been hampered by the lack of a high-resolution structural description of the extended array. Here, we report a novel reconstitution of the array, involving the receptor signaling domain, histidine kinase CheA, and adaptor protein CheW, as well as a density map of the core-signaling unit at 11.3 Å resolution, obtained by cryo-electron tomography and sub-tomogram averaging. Extracting key structural constraints from our density map, we computationally construct and refine an atomic model of the core array structure, exposing novel interfaces between the component proteins. Using all-atom molecular dynamics simulations, we further reveal a distinctive conformational change in CheA. Mutagenesis and chemical cross-linking experiments confirm the importance of the conformational dynamics of CheA for chemotactic function. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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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_3234.map.gz | 71.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3234-v30.xml emd-3234.xml | 12.6 KB 12.6 KB | 表示 表示 | EMDBヘッダ |
画像 | EMD-3234.tif emd_3234.tif | 200.5 KB 200.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3234 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3234 | HTTPS FTP |
-関連構造データ
関連構造データ | 6319C 6320C 3ja6C 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
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_3234.map.gz / 形式: CCP4 / 大きさ: 75.4 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | The tomogram is is binned by 4 while those used in the corresponding subTomogram work were used at full sampling. The protein array is best viewed by rotating around the X-axis 3.3 degrees, and the Y-axis 0.3 degrees as Imod Slicer angles. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 12.04 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
-試料の構成要素
-全体 : tarCF CheA CheW
全体 | 名称: tarCF CheA CheW |
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要素 |
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-超分子 #1000: tarCF CheA CheW
超分子 | 名称: tarCF CheA CheW / タイプ: sample / ID: 1000 集合状態: Trimer of (CheA dimer, dimer of tarCF trimers of dimers, 2 CheW subunits) Number unique components: 3 |
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分子量 | 理論値: 1.66 MDa |
-分子 #1: Chemotaxis protein CheA
分子 | 名称: Chemotaxis protein CheA / タイプ: protein_or_peptide / ID: 1 / Name.synonym: Bacterial Chemotaxis Histidine Kinase CheA / コピー数: 6 / 集合状態: Dimer / 組換発現: Yes |
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由来(天然) | 生物種: Escherichia coli (大腸菌) / 細胞中の位置: Inner Membrane |
分子量 | 理論値: 71.384 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) / 組換株: RP3098 / 組換プラスミド: pKJ9 |
配列 | UniProtKB: Chemotaxis protein CheA |
-分子 #2: Chemotaxis protein CheW
分子 | 名称: Chemotaxis protein CheW / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 集合状態: monomeric / 組換発現: Yes |
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由来(天然) | 生物種: Escherichia coli (大腸菌) / 細胞中の位置: Inner Membrane |
分子量 | 理論値: 18.083 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) / 組換株: RP3098 / 組換プラスミド: PPA770 |
配列 | UniProtKB: Chemotaxis protein CheW |
-分子 #3: Methyl-accepting chemotaxis protein II
分子 | 名称: Methyl-accepting chemotaxis protein II / タイプ: protein_or_peptide / ID: 3 / Name.synonym: tarCF 詳細: Cytoplasmic fragment of wild-type aspartate receptor コピー数: 6 / 集合状態: trimer of dimers / 組換発現: Yes |
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由来(天然) | 生物種: Escherichia coli (大腸菌) / 細胞中の位置: Inner Membrane |
分子量 | 理論値: 31.209 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) / 組換株: RP3098 / 組換プラスミド: pHTCF |
配列 | UniProtKB: Methyl-accepting chemotaxis protein II |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 電子線トモグラフィー法 |
試料の集合状態 | 2D array |
-試料調製
緩衝液 | pH: 7.4 / 詳細: 75 mM Tris-HCl, 100 mM KCl, 5 mM MgCl2 |
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グリッド | 詳細: Perforated R2/2 Quantifoil grids precoated with 10 nm fiducial gold beads on the backside of the grid |
凍結 | 凍結剤: ETHANE / 装置: HOMEMADE PLUNGER 手法: Single-sided blotting to avoid disruption of the monolayer |
詳細 | Pseudo-crystalline 2D monolayer reconstituted on a lipid monolayer |
-電子顕微鏡法
顕微鏡 | FEI POLARA 300 |
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日付 | 2009年1月7日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) 実像数: 60 / 平均電子線量: 60 e/Å2 / ビット/ピクセル: 16 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 49834 / 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD / Cs: 2.0 mm / 最大 デフォーカス(公称値): 8.0 µm / 最小 デフォーカス(公称値): 4.0 µm / 倍率(公称値): 39000 |
試料ステージ | 試料ホルダーモデル: OTHER / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 ° / Tilt series - Axis1 - Angle increment: 3 ° |
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
-画像解析
詳細 | CTF correction (phase only) performed on projections rotated to have tilt axis coincide with Y-axis. Projections aligned using area matching with geometry refinement in Protomo. Reconstruction with SIRT in IMOD. |
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最終 再構成 | アルゴリズム: OTHER / 解像度の算出法: OTHER / ソフトウェア - 名称: IMOD / 使用した粒子像数: 60 |
CTF補正 | 詳細: TomoCTF (strip-based periodogram) |
結晶パラメータ | 面群: P 1 |