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基本情報
登録情報 | データベース: EMDB / ID: EMD-2325 | |||||||||
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タイトル | Visualizing GroEL/ES in the Act of Encapsulating a Non-Native Substrate Protein | |||||||||
![]() | C7-symmetry imposed 3D reconstruction of the bullet-shaped subpopulation sorted from the heterogeneous sample of EL43Py reacted with GroES and nucleotide ATP | |||||||||
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![]() | protein folding / chaperonin / GroEL / GroEL-GroES / cryo-EM / heterogeneity | |||||||||
機能・相同性 | ![]() GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein-folding chaperone binding / protein refolding / response to heat / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / metal ion binding / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 8.9 Å | |||||||||
![]() | Chen D-H / Madan D / Weaver J / Lin Z / Schroder GF / Chiu W / Rye HS | |||||||||
![]() | ![]() タイトル: Visualizing GroEL/ES in the act of encapsulating a folding protein. 著者: Dong-Hua Chen / Damian Madan / Jeremy Weaver / Zong Lin / Gunnar F Schröder / Wah Chiu / Hays S Rye / ![]() 要旨: The GroEL/ES chaperonin system is required for the assisted folding of many proteins. How these substrate proteins are encapsulated within the GroEL-GroES cavity is poorly understood. Using symmetry- ...The GroEL/ES chaperonin system is required for the assisted folding of many proteins. How these substrate proteins are encapsulated within the GroEL-GroES cavity is poorly understood. Using symmetry-free, single-particle cryo-electron microscopy, we have characterized a chemically modified mutant of GroEL (EL43Py) that is trapped at a normally transient stage of substrate protein encapsulation. We show that the symmetric pattern of the GroEL subunits is broken as the GroEL cis-ring apical domains reorient to accommodate the simultaneous binding of GroES and an incompletely folded substrate protein (RuBisCO). The collapsed RuBisCO folding intermediate binds to the lower segment of two apical domains, as well as to the normally unstructured GroEL C-terminal tails. A comparative structural analysis suggests that the allosteric transitions leading to substrate protein release and folding involve concerted shifts of GroES and the GroEL apical domains and C-terminal tails. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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マップデータ | ![]() | 19.8 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 15.4 KB 15.4 KB | 表示 表示 | ![]() |
画像 | ![]() | 254 KB | ||
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EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | C7-symmetry imposed 3D reconstruction of the bullet-shaped subpopulation sorted from the heterogeneous sample of EL43Py reacted with GroES and nucleotide ATP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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試料の構成要素
-全体 : GroEL variant EL43Py capped by GroES with the assistance of nucle...
全体 | 名称: GroEL variant EL43Py capped by GroES with the assistance of nucleotide ATP |
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要素 |
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-超分子 #1000: GroEL variant EL43Py capped by GroES with the assistance of nucle...
超分子 | 名称: GroEL variant EL43Py capped by GroES with the assistance of nucleotide ATP タイプ: sample / ID: 1000 / 詳細: The molecule is bullet-shaped 集合状態: One heptamer of GroES and seven nucleotides of ATP binds to one tetradecamer of GroEL variant EL43Py Number unique components: 3 |
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分子量 | 実験値: 870 KDa / 理論値: 870 KDa 手法: GroEL molecular weight 800kDa plus GroES molecular weight 70kDa |
-分子 #1: GroELcys0-D398A-S43C-pyrene
分子 | 名称: GroELcys0-D398A-S43C-pyrene / タイプ: protein_or_peptide / ID: 1 / Name.synonym: EL398A43Py 詳細: A GroEL variant in which the endogenous Cys residues (138, 458, 519) have been changed to Ala (GroELcys0) was modified to contain two additional mutations: D398A and S43C. The D398A mutation ...詳細: A GroEL variant in which the endogenous Cys residues (138, 458, 519) have been changed to Ala (GroELcys0) was modified to contain two additional mutations: D398A and S43C. The D398A mutation prevents ATP hydrolysis by GroEL, while the S43C mutation, located at the tip of stem loop at the bottom of the GroEL cavity, permits the covalent attachment of N-1-pyrene maleimide to this position. コピー数: 14 / 集合状態: Tetradecamer / 組換発現: Yes |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 実験値: 800 KDa / 理論値: 800 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | UniProtKB: Chaperonin GroEL |
-分子 #2: GroES
分子 | 名称: GroES / タイプ: protein_or_peptide / ID: 2 / コピー数: 7 / 集合状態: Heptamer / 組換発現: Yes |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 実験値: 70 KDa / 理論値: 70 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | UniProtKB: Co-chaperonin GroES |
-分子 #3: Adenosine triphosphate
分子 | 名称: Adenosine triphosphate / タイプ: ligand / ID: 3 / Name.synonym: ATP / コピー数: 7 / 組換発現: No |
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由来(天然) | 生物種: synthetic construct (人工物) |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 6.4 mg/mL |
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緩衝液 | pH: 7.6 / 詳細: 50 mM Hepes, 5 mM KOAc, 10 mM Mg(OAc)2, 2 mM DTT |
グリッド | 詳細: 400 mesh R1.2/1.3 Quantifoil grid glow-discharged 10 sec before freezing |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 98 K / 装置: FEI VITROBOT MARK III / 手法: Blot for 1 second before plunging |
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電子顕微鏡法
顕微鏡 | JEOL 3000SFF |
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温度 | 最低: 10 K / 最高: 12 K / 平均: 11 K |
アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected at 400,000 times magnification |
日付 | 2007年3月7日 |
撮影 | カテゴリ: FILM / フィルム・検出器のモデル: KODAK SO-163 FILM デジタル化 - スキャナー: NIKON SUPER COOLSCAN 9000 デジタル化 - サンプリング間隔: 6.35 µm / 実像数: 390 / 平均電子線量: 36 e/Å2 / 詳細: The scanned images were averaged twice. / ビット/ピクセル: 8 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 61060 / 照射モード: FLOOD BEAM / 撮影モード: OTHER / Cs: 1.6 mm / 最大 デフォーカス(公称値): 3.5 µm / 最小 デフォーカス(公称値): 1.2 µm / 倍率(公称値): 60000 |
試料ステージ | 試料ホルダー: Helium cooled top-entry cartridge / 試料ホルダーモデル: JEOL |
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画像解析
-原子モデル構築 1
初期モデル | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: J / Chain - #10 - Chain ID: K / Chain - #11 - Chain ID: L / Chain - #12 - Chain ID: M / Chain - #13 - Chain ID: N / Chain - #14 - Chain ID: O / Chain - #15 - Chain ID: P / Chain - #16 - Chain ID: Q / Chain - #17 - Chain ID: R / Chain - #18 - Chain ID: S / Chain - #19 - Chain ID: T / Chain - #20 - Chain ID: U |
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ソフトウェア | 名称: DireX |
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT 当てはまり具合の基準: cross-correlation coefficient |
得られたモデル | ![]() PDB-3zpz: |