+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0737 | |||||||||
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タイトル | 2-start helix structure of SBA/GN3GN microtube with a diameter of about 29 nm | |||||||||
マップデータ | SBA/GN3GN microtube | |||||||||
試料 |
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生物種 | Glycine max (ダイズ) | |||||||||
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: 13.1 Å | |||||||||
データ登録者 | Zhang L / Chen GS / Chen SY | |||||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: J Am Chem Soc / 年: 2019 タイトル: Chemically Controlled Helical Polymorphism in Protein Tubes by Selective Modulation of Supramolecular Interactions. 著者: Zhen Li / Shuyu Chen / Chendi Gao / Zhiwei Yang / Kuo-Chih Shih / Zdravko Kochovski / Guang Yang / Lu Gou / Mu-Ping Nieh / Ming Jiang / Lei Zhang / Guosong Chen / 要旨: Polymorphism has been the subject of investigation across different research disciplines. In biology, polymorphism could be interpreted in such a way that discrete biomacromolecules can adopt ...Polymorphism has been the subject of investigation across different research disciplines. In biology, polymorphism could be interpreted in such a way that discrete biomacromolecules can adopt diversiform specific conformations/packing arrangement, and this polymorph-dependent property is essential for many biochemical processes. For example, bacterial flagellar filament, composed of flagellin, switches between different supercoiled state allowing the bacteria to swim and tumble. However, in artificial supramolecular systems, it is often challenging to achieve polymorph control and prediction, and in most cases, two or more concomitant polymorphs of similar formation energies coexist. Here, we show that a tetrameric protein with properly oriented binding sites on its surface can arrange into diverse protein tubes with distinct helical parameters by adding specifically designed inducing ligands. We examined several parameters of the ligand that would influence the protein tube formation and found that the flexibility of the ligand linker and the dimerization pose of the ligand complex is critical for the successful production of the tubes and eventually influence the specific helical polymorphs of the formed tubes. A surface lattice accommodation model was further developed to rationalize the geometrical relationship between each helical tube type. Molecular simulation was used to elucidate the interactions between ligands and SBA and molecular basis for polymorphic switching of the protein tubes. Moreover, the kinetics of structural formation was studied and the ligand design was found that can affect the kinetics of the protein polymerization pathway. In short, our designed protein tubes serves as an enlightening system for understanding how a protein polymer composed of a single protein switches among different helical states. | |||||||||
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_0737.map.gz | 58.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0737-v30.xml emd-0737.xml | 8.1 KB 8.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_0737_fsc.xml | 9.3 KB | 表示 | FSCデータファイル |
画像 | emd_0737.png | 67.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0737 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0737 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0737_validation.pdf.gz | 78.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0737_full_validation.pdf.gz | 77.9 KB | 表示 | |
XML形式データ | emd_0737_validation.xml.gz | 493 B | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0737 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0737 | 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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-マップ
ファイル | ダウンロード / ファイル: emd_0737.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | SBA/GN3GN microtube | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.051 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 : Helical complex of soybean agglutinin protein with GN3GN ligand
全体 | 名称: Helical complex of soybean agglutinin protein with GN3GN ligand |
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要素 |
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-超分子 #1: Helical complex of soybean agglutinin protein with GN3GN ligand
超分子 | 名称: Helical complex of soybean agglutinin protein with GN3GN ligand タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1 |
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由来(天然) | 生物種: Glycine max (ダイズ) |
-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: 7.2 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TALOS ARCTICA |
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撮影 | フィルム・検出器のモデル: FEI CETA (4k x 4k) / 平均電子線量: 30.0 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |