+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1ucu | ||||||
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タイトル | R-type straight flagellar filament made of full-length flagellin | ||||||
要素 | phase 1 Flagellin | ||||||
キーワード | STRUCTURAL PROTEIN (タンパク質) / FLAGELLIN (フラジェリン) / FLAGELLAR FILAMENT / HELICAL RECONSTRUCTION | ||||||
機能・相同性 | 機能・相同性情報 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 | Salmonella typhimurium (サルモネラ菌) | ||||||
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 | ||||||
データ登録者 | Yonekura, K. / Maki-Yonekura, S. / Namba, K. | ||||||
引用 | ジャーナル: Nature / 年: 2003 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. #1: ジャーナル: NATURE / 年: 2001 タイトル: Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling 著者: Samatey, F.A. / Imada, K. / Nagashima, S. / Vonderviszt, F. / Kumasaka, T. / Yamamoto, M. / Namba, K. | ||||||
履歴 |
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Remark 244 | OTHER_DETAILS: REPEAT DISTANCE (ANGSTROMS) : 1698.8 BASIC HELIX INDEX (N10, L10) : ( 11, 4) (N01, ... OTHER_DETAILS: REPEAT DISTANCE (ANGSTROMS) : 1698.8 BASIC HELIX INDEX (N10, L10) : ( 11, 4) (N01, L01) : ( -5, 31) SELECTION RULE : L = 66 N + 361 M MAXIMUM BESSEL ORDER : 170 NUMBER OF LAYER-LINES : 298 NUMBER OF FILAMENT IMAGES : 102 NUMBER OF MOLECULAR IMAGES : 41,469 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.000 ALONG THE MERIDIAN EFFECTIVE RESOLUTION (ANGSTROMS) : 5.000 ALONG THE EQUATOR | ||||||
Remark 650 | HELIX Determination method: Author determined | ||||||
Remark 700 | SHEET Determination method: Author determined |
-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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1ucu.cif.gz | 88.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1ucu.ent.gz | 65.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1ucu.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/uc/1ucu ftp://data.pdbj.org/pub/pdb/validation_reports/uc/1ucu | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 51551.203 Da / 分子数: 1 / 変異: A449V / 由来タイプ: 天然 由来: (天然) Salmonella typhimurium (サルモネラ菌) 株: SJW 1665 / 参照: UniProt: P06179 |
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-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 |
-試料調製
構成要素 | 名称: R-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) |
結晶化 | *PLUS 手法: unknown |
-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: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 50000 X / 倍率(補正後): 47600 X / 最大 デフォーカス(公称値): 2200 nm / 最小 デフォーカス(公称値): 1100 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 |
-解析
ソフトウェア |
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EMソフトウェア | 名称: X-PLOR / カテゴリ: モデルフィッティング | ||||||||||||
CTF補正 | 詳細: BOTH AMPLITUDE AND PHASE | ||||||||||||
3次元再構成 | 手法: HELICAL RECONSTRUCTION / 解像度: 4 Å / 粒子像の数: 102 / ピクセルサイズ(公称値): 1 Å / ピクセルサイズ(実測値): 1.05 Å / 倍率補正: R-TYPE STRAIGHT FLAGELLAR FILAMENT 詳細: The atomic model of a flagellin fragment F41 from Samatey et al (2001) NATURE 410 331-337 (PDB ENTRY 1IO1) was fitted to the density map using O. Then, initial model of full-length flagellin ...詳細: The atomic model of a flagellin fragment F41 from Samatey et al (2001) NATURE 410 331-337 (PDB ENTRY 1IO1) was fitted to the density map using O. Then, initial model of full-length flagellin was built by tracing missing terminal chains. The model was refined using both positional and simulated annealing refinements, by a molecular dynamics refinement program, FEX-PLOR, which we developed based on FX-PLOR for EM image analysis of the helical assembly. The amplitude-weighted phase-residual was implemented as an effective potential energy. The layer-line amplitude distributions of the EM data were then scaled to the structure factors calculated from the model based on their radial amplitude profiles obtained by averaging the amplitudes within each resolution shell. The density map was calculated again, and model building and refinement were iterated. 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 | ||||||||||||
原子モデル構築 | PDB-ID: 1IO1 Accession code: 1IO1 / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化 | 解像度: 4→30 Å / Rfactor Rwork: 0.3 | ||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 4→30 Å
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