+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 3b5u | ||||||
---|---|---|---|---|---|---|---|
タイトル | Actin filament model from extended form of acromsomal bundle in the Limulus sperm | ||||||
![]() | Actin, alpha skeletal muscle | ||||||
![]() | MOTOR PROTEIN / ACTIN FILAMENT / ACTIN / ACROMSOMAL BUNDLE / CRYOEM | ||||||
機能・相同性 | ![]() cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly ...cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | 電子線結晶学 / クライオ電子顕微鏡法 / 解像度: 9.5 Å | ||||||
![]() | Cong, Y. / Topf, M. / Sali, A. / Matsudaira, P. / Dougherty, M. / Chiu, W. / Schmid, M.F. | ||||||
![]() | ![]() タイトル: Crystallographic conformers of actin in a biologically active bundle of filaments. 著者: Yao Cong / Maya Topf / Andrej Sali / Paul Matsudaira / Matthew Dougherty / Wah Chiu / Michael F Schmid / ![]() 要旨: Actin carries out many of its cellular functions through its filamentous form; thus, understanding the detailed structure of actin filaments is an essential step in achieving a mechanistic ...Actin carries out many of its cellular functions through its filamentous form; thus, understanding the detailed structure of actin filaments is an essential step in achieving a mechanistic understanding of actin function. The acrosomal bundle in the Limulus sperm has been shown to be a quasi-crystalline array with an asymmetric unit composed of a filament with 14 actin-scruin pairs. The bundle in its true discharge state penetrates the jelly coat of the egg. Our previous electron crystallographic reconstruction demonstrated that the actin filament cross-linked by scruin in this acrosomal bundle state deviates significantly from a perfect F-actin helix. In that study, the tertiary structure of each of the 14 actin protomers in the asymmetric unit of the bundle filament was assumed to be constant. In the current study, an actin filament atomic model in the acrosomal bundle has been refined by combining rigid-body docking with multiple actin crystal structures from the Protein Data Bank and constrained energy minimization. Our observation demonstrates that actin protomers adopt different tertiary conformations when they form an actin filament in the bundle. The scruin and bundle packing forces appear to influence the tertiary and quaternary conformations of actin in the filament of this biologically active bundle. | ||||||
履歴 |
|
-
構造の表示
ムービー |
![]() |
---|---|
構造ビューア | 分子: ![]() ![]() |
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 812.5 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 644.7 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 892.5 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 1.1 MB | 表示 | |
XML形式データ | ![]() | 146.2 KB | 表示 | |
CIF形式データ | ![]() | 220 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
-
集合体
登録構造単位 | ![]()
|
---|---|
1 |
|
-
要素
#1: タンパク質 | 分子量: 42096.953 Da / 分子数: 14 / 由来タイプ: 天然 詳細: Holmes Actin model from Fiber Diffraction experiment 由来: (天然) ![]() ![]() |
---|
-実験情報
-実験
実験 | 手法: 電子線結晶学 |
---|---|
EM実験 | 試料の集合状態: 3D ARRAY / 3次元再構成法: 電子線結晶学 |
-
試料調製
構成要素 |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
緩衝液 | pH: 7.4 / 詳細: see J Mol Biol, 221, 711-725 (1991) | |||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | |||||||||||||||
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE |
-データ収集
顕微鏡 | モデル: JEOL 4000EX 詳細: For more information, please refer to EMDB entry EMD-1088 http://www.ebi.ac.uk/msd-srv/emsearch/atlas/1088_summary.html |
---|---|
電子銃 | 電子線源: LAB6 / 加速電圧: 400 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 40000 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 800 nm |
試料ホルダ | 温度: 106 K |
撮影 | 電子線照射量: 15 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
-
解析
EMソフトウェア |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3次元再構成 | 手法: Cross-correlation and merging of crystallographic reflections derived from cryoelectron micrographs of 3D crystals. For more information, please refer to EMDB entry EMD-1088 http://www.ebi.ac. ...手法: Cross-correlation and merging of crystallographic reflections derived from cryoelectron micrographs of 3D crystals. For more information, please refer to EMDB entry EMD-1088 http://www.ebi.ac.uk/msd-srv/emsearch/atlas/1088_summary.html 解像度: 9.5 Å / 解像度の算出法: DIFFRACTION PATTERN/LAYERLINES 詳細: Cross-correlation and merging of crystallographic reflections derived from cryoelectron micrographs of 3D crystalss: application to the Limulus acrosomal bundle, Michael F. Schmid, J. Struc. ...詳細: Cross-correlation and merging of crystallographic reflections derived from cryoelectron micrographs of 3D crystalss: application to the Limulus acrosomal bundle, Michael F. Schmid, J. Struc. Biol., 144 (2003) 195-208 対称性のタイプ: 3D CRYSTAL | ||||||||||||
原子モデル構築 | プロトコル: AB INITIO MODEL / 空間: REAL Target criteria: Best cross-correlation score between model and cryoEM map 詳細: REFINEMENT PROTOCOL--Foldhunter program from EMAN single particle analysis package | ||||||||||||
原子モデル構築 | 詳細: Holmes' Actin model from Fiber Diffraction experiment | ||||||||||||
精密化ステップ | サイクル: LAST
|