+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2071 | |||||||||
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タイトル | Gating movement in acetylcholine receptor analysed by time-resolved electron cryo-microscopy | |||||||||
マップデータ | Density map of acetylcholine receptor | |||||||||
試料 |
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キーワード | acetylcholine receptor (アセチルコリン受容体) / freeze-trapping / asymmetric gating / allosteric mechanism | |||||||||
機能・相同性 | 機能・相同性情報 acetylcholine-gated channel complex / acetylcholine-gated monoatomic cation-selective channel activity / acetylcholine receptor signaling pathway / transmembrane signaling receptor activity / postsynaptic membrane 類似検索 - 分子機能 | |||||||||
生物種 | Torpedo marmorata (エイ) | |||||||||
手法 | らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 6.2 Å | |||||||||
データ登録者 | Unwin N / Fujiyoshi Y | |||||||||
引用 | ジャーナル: J Mol Biol / 年: 2012 タイトル: Gating movement of acetylcholine receptor caught by plunge-freezing. 著者: Nigel Unwin / Yoshinori Fujiyoshi / 要旨: The nicotinic acetylcholine (ACh) receptor converts transiently to an open-channel form when activated by ACh released into the synaptic cleft. We describe here the conformational change underlying ...The nicotinic acetylcholine (ACh) receptor converts transiently to an open-channel form when activated by ACh released into the synaptic cleft. We describe here the conformational change underlying this event, determined by electron microscopy of ACh-sprayed and freeze-trapped postsynaptic membranes. ACh binding to the α subunits triggers a concerted rearrangement in the ligand-binding domain, involving an ~1-Å outward displacement of the extracellular portion of the β subunit where it interacts with the juxtaposed ends of α-helices shaping the narrow membrane-spanning pore. The β-subunit helices tilt outward to accommodate this displacement, destabilising the arrangement of pore-lining helices, which in the closed channel bend inward symmetrically to form a central hydrophobic gate. Straightening and tangential motion of the pore-lining helices effect channel opening by widening the pore asymmetrically and increasing its polarity in the region of the gate. The pore-lining helices of the α(γ) and δ subunits, by flexing between alternative bent and straight conformations, undergo the greatest movements. This coupled allosteric transition shifts the structure from a tense (closed) state toward a more relaxed (open) state. | |||||||||
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_2071.map.gz | 2.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-2071-v30.xml emd-2071.xml | 13 KB 13 KB | 表示 表示 | EMDBヘッダ |
画像 | emd-2071.tif | 185.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2071 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2071 | HTTPS FTP |
-関連構造データ
-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_2071.map.gz / 形式: CCP4 / 大きさ: 10.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Density map of acetylcholine receptor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1 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 : nicotinic acetylcholine receptor in native postsynaptic membrane ...
全体 | 名称: nicotinic acetylcholine receptor in native postsynaptic membrane from Torpedo marmorata |
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要素 |
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-超分子 #1000: nicotinic acetylcholine receptor in native postsynaptic membrane ...
超分子 | 名称: nicotinic acetylcholine receptor in native postsynaptic membrane from Torpedo marmorata タイプ: sample / ID: 1000 / 集合状態: 5 subunits / Number unique components: 1 |
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分子量 | 実験値: 300 KDa / 理論値: 300 KDa 手法: molecular weight based on amino acid sequence data and attached sugars |
-分子 #1: nicotinic acetylcholine receptor
分子 | 名称: nicotinic acetylcholine receptor / タイプ: protein_or_peptide / ID: 1 / Name.synonym: nicotinic receptor 詳細: Protein is embedded in postsynaptic membrane isolated from Torpedo marmorata electric organ 集合状態: pentamer / 組換発現: No / データベース: NCBI |
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由来(天然) | 生物種: Torpedo marmorata (エイ) / 別称: marbled electric ray / 組織: electric organ / 細胞: electrocyte cells / Organelle: plasma membrane / 細胞中の位置: plasma membrane |
分子量 | 実験値: 300 KDa / 理論値: 300 KDa |
-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 | らせん対称体再構成法 |
試料の集合状態 | helical array |
-試料調製
緩衝液 | pH: 7 / 詳細: 100 mM sodium cacodylate, 1 mM calcium chloride |
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グリッド | 詳細: 300 mesh copper grid with pre-irradiated thick holey carbon support, glow discharged in amylamine atmosphere |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 85 % / チャンバー内温度: 120 K / 装置: HOMEMADE PLUNGER 詳細: Vitrification carried out at an ambient temperature of 8 degrees C Timed resolved state: Vitrified within 10ms of exposure to acetylcholine (applied as the grid is being plunged,using a fine, focussed spray positioned about 1cm above the ethane surface) 手法: Blot until applied droplet loses contact with filter paper (indicated by loss of transparency; typically 6s) |
詳細 | Tubular membrane crystals of acetylcholine receptors grow spontaneously from isolated postsynaptic membranes when incubated in low salt buffer at 17 degrees C for two weeks |
-電子顕微鏡法
顕微鏡 | JEOL 3000SFF |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 38500 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 1.6 mm / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.9 µm / 倍率(公称値): 40000 |
試料ステージ | 試料ホルダー: Top-entry holder for liquid helium cooled stage (the temperature of the specimen in this holder is usually at 4K) 試料ホルダーモデル: OTHER |
温度 | 最低: 10 K / 最高: 20 K / 平均: 10 K |
アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected based on appearance of carbon film at 250,000 times magnification |
詳細 | Standard low dose imaging of specimens over holes in the carbon support film |
日付 | 2005年11月1日 |
撮影 | カテゴリ: FILM / フィルム・検出器のモデル: KODAK SO-163 FILM / デジタル化 - スキャナー: OTHER / デジタル化 - サンプリング間隔: 2.5 µm / 実像数: 111 / 平均電子線量: 25 e/Å2 詳細: All images recorded on film, developed in Kodak d19 developer Od range: 1 / ビット/ピクセル: 16 |
-画像解析
CTF補正 | 詳細: Each tube image |
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最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 6.2 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: MRC, and, own, programs 詳細: Final maps were calculated from 111 tube images(closed class) and 123 tube images (open class) |
詳細 | Alignment and distortion correction of each tube image was done using a segmental Fourier-Bessel method (Beroukhim & Unwin (1997) Ultramicroscopy, 70:57-81) with 50% overlap between successive segments |
-原子モデル構築 1
初期モデル | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E |
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ソフトウェア | 名称: DireX |
詳細 | Protocol: Maximisation of correlation between experimental densities and atomic model, using a deformable elastic network algorithm. Identical refinement procedures were applied to both density maps. The fits were validated by applying the same refinement procedures to independent density maps calculated from half-datasets |
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
得られたモデル | PDB-4aq5: |