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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: 3los | |||||||||
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タイトル | Atomic Model of Mm-cpn in the Closed State | |||||||||
![]() | Chaperonin | |||||||||
![]() | CHAPERONE / Group II chaperonin / Protein Folding / Mm-cpn / Single Particle Reconstruction / Methanococcus maripaludis / ATP-binding / Nucleotide-binding | |||||||||
機能・相同性 | ![]() chaperonin-containing T-complex / ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.3 Å | |||||||||
![]() | Zhang, J. / Baker, M.L. / Schroeder, G. / Douglas, N.R. / Reissmann, S. / Jakana, J. / Dougherty, M. / Fu, C.J. / Levitt, M. / Ludtke, S.J. ...Zhang, J. / Baker, M.L. / Schroeder, G. / Douglas, N.R. / Reissmann, S. / Jakana, J. / Dougherty, M. / Fu, C.J. / Levitt, M. / Ludtke, S.J. / Frydman, J. / Chiu, W. | |||||||||
![]() | ![]() タイトル: Mechanism of folding chamber closure in a group II chaperonin. 著者: Junjie Zhang / Matthew L Baker / Gunnar F Schröder / Nicholai R Douglas / Stefanie Reissmann / Joanita Jakana / Matthew Dougherty / Caroline J Fu / Michael Levitt / Steven J Ludtke / Judith Frydman / Wah Chiu / ![]() 要旨: Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings ...Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states. The 4.3 A resolution of the closed conformation allowed building of the first ever atomic model directly from the single particle cryo-EM density map, in which we were able to visualize the nucleotide and more than 70% of the side chains. The model of the open conformation was obtained by using the deformable elastic network modelling with the 8 A resolution open-state cryo-EM density restraints. Together, the open and closed structures show how local conformational changes triggered by ATP hydrolysis lead to an alteration of intersubunit contacts within and across the rings, ultimately causing a rocking motion that closes the ring. Our analyses show that there is an intricate and unforeseen set of interactions controlling allosteric communication and inter-ring signalling, driving the conformational cycle of group II chaperonins. Beyond this, we anticipate that our methodology of combining single particle cryo-EM and computational modelling will become a powerful tool in the determination of atomic details involved in the dynamic processes of macromolecular machines in solution. | |||||||||
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構造の表示
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構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 1.3 MB | 表示 | ![]() |
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PDB形式 | ![]() | 1 MB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2.1 MB | 表示 | |
XML形式データ | ![]() | 357.4 KB | 表示 | |
CIF形式データ | ![]() | 498.9 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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対称性 | 点対称性: (シェーンフリース記号: D8 (2回x8回 2面回転対称)) |
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要素
#1: タンパク質 | 分子量: 58290.262 Da / 分子数: 16 / 由来タイプ: 組換発現 由来: (組換発現) ![]() 遺伝子: hsp60, MMP1515 / 発現宿主: ![]() ![]() Has protein modification | Y | |
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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: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 |
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分子量 | 値: 0.96 MDa / 実験値: NO | |||||||||||||||
緩衝液 | 名称: ATPase buffer / pH: 7.5 / 詳細: ATPase buffer | |||||||||||||||
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: FEI VITROBOT MARK I / 凍結剤: ETHANE / 湿度: 100 % / 手法: 1 blot 3 seconds |
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電子顕微鏡撮影
顕微鏡 | モデル: JEOL 3200FSC |
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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): 80000 X / 倍率(補正後): 112000 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): 1000 nm / Cs: 4.1 mm 非点収差: objective lens astigmatism was corrected at 100,000 times magnification カメラ長: 0 mm |
試料ホルダ | 試料ホルダーモデル: JEOL 3200FSC CRYOHOLDER / 資料ホルダタイプ: side-entry / 温度: 100 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: GATAN ULTRASCAN 4000 (4k x 4k) |
電子光学装置 | エネルギーフィルター名称: In-column Omega Filter エネルギーフィルター 上限: 10 eV / エネルギーフィルター 下限: 0 eV |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M |
放射波長 | 相対比: 1 |
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解析
EMソフトウェア | 名称: EMAN / カテゴリ: 3次元再構成 | ||||||||||||
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CTF補正 | 詳細: Each micrograph | ||||||||||||
対称性 | 点対称性: D8 (2回x8回 2面回転対称) | ||||||||||||
3次元再構成 | 手法: Projection-match / 解像度: 4.3 Å / 解像度の算出法: FSC 0.5 CUT-OFF 詳細: THE SINGLE SUBUNIT MODEL OF MM-CPN WAS MANUALLY BUILT IN THE CRYO-EM DENSITY USING COOT. THE ENTIRE 16-SUBUNIT COMPLEX WAS GENERATED BASED ON THE D8 SYMMETRY. 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | 詳細: DETAILS--THE SINGLE SUBUNIT MODEL OF MM-CPN WAS MANUALLY BUILT IN THE CRYO-EM DENSITY USING COOT. THE ENTIRE 16-SUBUNIT COMPLEX WAS GENERATED BASED ON THE D8 SYMMETRY. | ||||||||||||
精密化ステップ | サイクル: LAST
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