- PDB-4a0o: Symmetry-free cryo-EM map of TRiC in the nucleotide-free (apo) state -
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基本情報
登録情報
データベース: PDB / ID: 4a0o
タイトル
Symmetry-free cryo-EM map of TRiC in the nucleotide-free (apo) state
要素
T-COMPLEX PROTEIN 1 SUBUNIT BETA
キーワード
CHAPERONE / CHAPERONIN / PROTEIN FOLDING
機能・相同性
機能・相同性情報
Association of TriC/CCT with target proteins during biosynthesis / RHOBTB2 GTPase cycle / RHOBTB1 GTPase cycle / chaperonin-containing T-complex / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding 類似検索 - 分子機能
ジャーナル: EMBO J / 年: 2012 タイトル: Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle. 著者: Yao Cong / Gunnar F Schröder / Anne S Meyer / Joanita Jakana / Boxue Ma / Matthew T Dougherty / Michael F Schmid / Stefanie Reissmann / Michael Levitt / Steven L Ludtke / Judith Frydman / Wah Chiu / 要旨: The eukaryotic group II chaperonin TRiC/CCT is a 16-subunit complex with eight distinct but similar subunits arranged in two stacked rings. Substrate folding inside the central chamber is triggered ...The eukaryotic group II chaperonin TRiC/CCT is a 16-subunit complex with eight distinct but similar subunits arranged in two stacked rings. Substrate folding inside the central chamber is triggered by ATP hydrolysis. We present five cryo-EM structures of TRiC in apo and nucleotide-induced states without imposing symmetry during the 3D reconstruction. These structures reveal the intra- and inter-ring subunit interaction pattern changes during the ATPase cycle. In the apo state, the subunit arrangement in each ring is highly asymmetric, whereas all nucleotide-containing states tend to be more symmetrical. We identify and structurally characterize an one-ring closed intermediate induced by ATP hydrolysis wherein the closed TRiC ring exhibits an observable chamber expansion. This likely represents the physiological substrate folding state. Our structural results suggest mechanisms for inter-ring-negative cooperativity, intra-ring-positive cooperativity, and protein-folding chamber closure of TRiC. Intriguingly, these mechanisms are different from other group I and II chaperonins despite their similar architecture.
モード: BRIGHT FIELD / 倍率(公称値): 50000 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): 1200 nm
試料ホルダ
温度: 101 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 °
撮影
電子線照射量: 18 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM
画像スキャン
デジタル画像の数: 700
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解析
EMソフトウェア
名称: DireX / カテゴリ: モデルフィッティング
対称性
点対称性: C1 (非対称)
3次元再構成
手法: PROJECTION MATCHING / 解像度: 10.5 Å / 粒子像の数: 47151 / ピクセルサイズ(公称値): 2.4 Å / ピクセルサイズ(実測値): 2.4 Å 詳細: OUR MODELS DO NOT INCLUDE SOME REGIONS OF THE APICAL DOMAIN IN SEVERAL SUBUNITS, BECAUSE THE MAP IN THOSE REGIONS WAS NOT VERY WELL RESOLVED DUE TO THE DYNAMIC NATURE OF THOSE SUBUNITS. WE ...詳細: OUR MODELS DO NOT INCLUDE SOME REGIONS OF THE APICAL DOMAIN IN SEVERAL SUBUNITS, BECAUSE THE MAP IN THOSE REGIONS WAS NOT VERY WELL RESOLVED DUE TO THE DYNAMIC NATURE OF THOSE SUBUNITS. WE FITTED THE MODEL WITH THE OCCUPANCY REFINEMENT FEATURE IN DIREX. THIS BASICALLY DETERMINES WHETHER THERE IS SUFFICIENT DENSITY FOR EACH RESIDUE OR IF THERE IS REDUCED OR MISSING DENSITY. THE OCCUPANCY IS VALUE BETWEEN 0 AND 1. WE WROTE THIS VALUE INTO THE B-FACTOR COLUMN AS 100X(1-OCCUPANCY). THIS RESEMBLES A B-FACTOR BUT IS NOT EXACTLY THE SAME. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1960. (DEPOSITION ID: 10235). 対称性のタイプ: POINT