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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 3a5x | ||||||
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タイトル | L-type straight flagellar filament made of full-length flagellin | ||||||
![]() | Flagellin | ||||||
![]() | STRUCTURAL PROTEIN / MOTOR PROTEIN / FLAGELLIN / FLAGELLAR FILAMENT / HELICAL RECONSTRUCTION / Bacterial flagellum / Secreted | ||||||
機能・相同性 | ![]() TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / The IPAF inflammasome / bacterial-type flagellum / structural molecule activity / extracellular region 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | 電子顕微鏡法 / らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 4 Å | ||||||
![]() | Maki-Yonekura, S. / Yonekura, K. / Namba, K. | ||||||
![]() | ![]() タイトル: Conformational change of flagellin for polymorphic supercoiling of the flagellar filament. 著者: Saori Maki-Yonekura / Koji Yonekura / Keiichi Namba / ![]() 要旨: The bacterial flagellar filament is a helical propeller rotated by the flagellar motor for bacterial locomotion. The filament is a supercoiled assembly of a single protein, flagellin, and is formed ...The bacterial flagellar filament is a helical propeller rotated by the flagellar motor for bacterial locomotion. The filament is a supercoiled assembly of a single protein, flagellin, and is formed by 11 protofilaments. For bacterial taxis, the reversal of motor rotation switches the supercoil between left- and right-handed, both of which arise from combinations of two distinct conformations and packing interactions of the L-type and R-type protofilaments. Here we report an atomic model of the L-type straight filament by electron cryomicroscopy and helical image analysis. Comparison with the R-type structure shows interesting features: an orientation change of the outer core domains (D1) against the inner core domains (D0) showing almost invariant orientation and packing, a conformational switching within domain D1, and the conformational flexibility of domains D0 and D1 with their spoke-like connection for tight molecular packing. #1: ![]() タイトル: Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling. 著者: F A Samatey / K Imada / S Nagashima / F Vonderviszt / T Kumasaka / M Yamamoto / K Namba / ![]() 要旨: The bacterial flagellar filament is a helical propeller constructed from 11 protofilaments of a single protein, flagellin. The filament switches between left- and right-handed supercoiled forms when ...The bacterial flagellar filament is a helical propeller constructed from 11 protofilaments of a single protein, flagellin. The filament switches between left- and right-handed supercoiled forms when bacteria switch their swimming mode between running and tumbling. Supercoiling is produced by two different packing interactions of flagellin called L and R. In switching from L to R, the intersubunit distance ( approximately 52 A) along the protofilament decreases by 0.8 A. Changes in the number of L and R protofilaments govern supercoiling of the filament. Here we report the 2.0 A resolution crystal structure of a Salmonella flagellin fragment of relative molecular mass 41,300. The crystal contains pairs of antiparallel straight protofilaments with the R-type repeat. By simulated extension of the protofilament model, we have identified possible switch regions responsible for the bi-stable mechanical switch that generates the 0.8 A difference in repeat distance. #2: ![]() タイトル: Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. 著者: Koji Yonekura / Saori Maki-Yonekura / Keiichi Namba / ![]() 要旨: The bacterial flagellar filament is a helical propeller for bacterial locomotion. It is a helical assembly of a single protein, flagellin, and its tubular structure is formed by 11 protofilaments in ...The bacterial flagellar filament is a helical propeller for bacterial locomotion. It is a helical assembly of a single protein, flagellin, and its tubular structure is formed by 11 protofilaments in two distinct conformations, L- and R-type, for supercoiling. The X-ray crystal structure of a flagellin fragment lacking about 100 terminal residues revealed the protofilament structure, but the full filament structure is still essential for understanding the mechanism of supercoiling and polymerization. Here we report a complete atomic model of the R-type filament by electron cryomicroscopy. A density map obtained from image data up to 4 A resolution shows the feature of alpha-helical backbone and some large side chains. The atomic model built on the map reveals intricate molecular packing and an alpha-helical coiled coil formed by the terminal chains in the inner core of the filament, with its intersubunit hydrophobic interactions having an important role in stabilizing the filament. | ||||||
履歴 |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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-検証レポート
文書・要旨 | ![]() | 546.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 560.1 KB | 表示 | |
XML形式データ | ![]() | 17.2 KB | 表示 | |
CIF形式データ | ![]() | 26.9 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-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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要素
#1: タンパク質 | 分子量: 51537.180 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() 株: SJW1660 / 参照: UniProt: P06179 |
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配列の詳細 | A NATURAL MUTATION AT THIS POSITION |
-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: FILAMENT / 3次元再構成法: らせん対称体再構成法 |
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試料調製
構成要素 | 名称: L-TYPE STRAIGHT FLAGELLAR FILAMENT / タイプ: COMPLEX |
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緩衝液 | 名称: 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL / pH: 7.8 / 詳細: 150MM NACL, 2MM MGCL2, 20MM TRIS-HCL, 2-5% GLYCEROL |
試料 | 濃度: 0.1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: QUANTIFOIL R1.2/1.3 (25 NM THICK) |
急速凍結 | 凍結剤: ETHANE |
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電子顕微鏡撮影
顕微鏡 | モデル: JEOL 3000SFF |
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電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 50000 X / 倍率(補正後): 50000 X / 最大 デフォーカス(公称値): 2220 nm / 最小 デフォーカス(公称値): 1080 nm / Cs: 1.6 mm |
試料ホルダ | 温度: 4 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 20 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 相対比: 1 |
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解析
ソフトウェア | 名称: FEX-PLOR / 分類: 精密化 | ||||||||||||
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EMソフトウェア |
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CTF補正 | 詳細: Both amplitude and phase | ||||||||||||
3次元再構成 | 手法: Helical reconstruction / 解像度: 4 Å / ピクセルサイズ(公称値): 1 Å / ピクセルサイズ(実測値): 1 Å / 倍率補正: L-TYPE STRAIGHT flagellar filament 詳細: The layer-line spacing of the L-type straight flagellar filament is more than twice longer than that of the R-type, and frozen-hydrated L-type filaments tended to be more curved. Hence, ...詳細: The layer-line spacing of the L-type straight flagellar filament is more than twice longer than that of the R-type, and frozen-hydrated L-type filaments tended to be more curved. Hence, straightening of images using bi-cubic spline was carried out at the first stage. The three-dimensional map was calculated by helical image reconstruction. An initial map produced from 70 filament images, corresponding to 51,272 molecular images, showed relatively poor connections of the ND0 helix and the NS loop. Hence, images showing an inter-particle phase residual against the initial average larger than 40 were excluded from the data set to be averaged. As a result, a three-dimensional map of a better quality was obtained. The number of filament images used for the final image reconstruction was 47, and the total number of molecular images was 36,842, which is consistent with an estimated number of molecular images required to achieve this resolution range. 対称性のタイプ: HELICAL | ||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: RECIPROCAL / Target criteria: AMPLITUDE-WEIGHTED PHASE RESIDUAL 詳細: REFINEMENT PROTOCOL--POSITIONAL AND SIMULATED ANNEALING | ||||||||||||
精密化 | 最高解像度: 4 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 4 Å
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