+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j9k | ||||||
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タイトル | Structure of Dark apoptosome in complex with Dronc CARD domain | ||||||
要素 |
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キーワード | APOPTOSIS / programmed cell death / caspase activation | ||||||
機能・相同性 | 機能・相同性情報 hemocyte development / nurse cell apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of humoral immune response / positive regulation of glial cell apoptotic process / head involution / Formation of apoptosome / embryonic development via the syncytial blastoderm / salivary gland histolysis / positive regulation of compound eye retinal cell programmed cell death ...hemocyte development / nurse cell apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of humoral immune response / positive regulation of glial cell apoptotic process / head involution / Formation of apoptosome / embryonic development via the syncytial blastoderm / salivary gland histolysis / positive regulation of compound eye retinal cell programmed cell death / melanization defense response / sarcosine catabolic process / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / central nervous system formation / metamorphosis / compound eye development / chaeta development / sperm individualization / autophagic cell death / apoptosome / programmed cell death involved in cell development / Neutrophil degranulation / CARD domain binding / programmed necrotic cell death / S-adenosylmethionine cycle / : / programmed cell death / triglyceride homeostasis / zymogen activation / dendrite morphogenesis / neuron remodeling / response to starvation / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / ectopic germ cell programmed cell death / determination of adult lifespan / response to gamma radiation / central nervous system development / ADP binding / neuron cellular homeostasis / endopeptidase activity / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ / positive regulation of apoptotic process / negative regulation of cell population proliferation / cysteine-type endopeptidase activity / apoptotic process / protein homodimerization activity / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | Drosophila melanogaster (キイロショウジョウバエ) | ||||||
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: 4.1 Å | ||||||
データ登録者 | Pang, Y. / Bai, X. / Yan, C. / Hao, Q. / Chen, Z. / Wang, J. / Scheres, S.H.W. / Shi, Y. | ||||||
引用 | ジャーナル: Genes Dev / 年: 2015 タイトル: Structure of the apoptosome: mechanistic insights into activation of an initiator caspase from Drosophila. 著者: Yuxuan Pang / Xiao-chen Bai / Chuangye Yan / Qi Hao / Zheqin Chen / Jia-Wei Wang / Sjors H W Scheres / Yigong Shi / 要旨: Apoptosis is executed by a cascade of caspase activation. The autocatalytic activation of an initiator caspase, exemplified by caspase-9 in mammals or its ortholog, Dronc, in fruit flies, is ...Apoptosis is executed by a cascade of caspase activation. The autocatalytic activation of an initiator caspase, exemplified by caspase-9 in mammals or its ortholog, Dronc, in fruit flies, is facilitated by a multimeric adaptor complex known as the apoptosome. The underlying mechanism by which caspase-9 or Dronc is activated by the apoptosome remains unknown. Here we report the electron cryomicroscopic (cryo-EM) structure of the intact apoptosome from Drosophila melanogaster at 4.0 Å resolution. Analysis of the Drosophila apoptosome, which comprises 16 molecules of the Dark protein (Apaf-1 ortholog), reveals molecular determinants that support the assembly of the 2.5-MDa complex. In the absence of dATP or ATP, Dronc zymogen potently induces formation of the Dark apoptosome, within which Dronc is efficiently activated. At 4.1 Å resolution, the cryo-EM structure of the Dark apoptosome bound to the caspase recruitment domain (CARD) of Dronc (Dronc-CARD) reveals two stacked rings of Dronc-CARD that are sandwiched between two octameric rings of the Dark protein. The specific interactions between Dronc-CARD and both the CARD and the WD40 repeats of a nearby Dark protomer are indispensable for Dronc activation. These findings reveal important mechanistic insights into the activation of initiator caspase by the apoptosome. | ||||||
履歴 |
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-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 | 3j9k.cif.gz | 3.1 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j9k.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 3j9k.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
文書・要旨 | 3j9k_validation.pdf.gz | 1.9 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3j9k_full_validation.pdf.gz | 2.2 MB | 表示 | |
XML形式データ | 3j9k_validation.xml.gz | 334.9 KB | 表示 | |
CIF形式データ | 3j9k_validation.cif.gz | 575.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j9/3j9k ftp://data.pdbj.org/pub/pdb/validation_reports/j9/3j9k | HTTPS FTP |
-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: 112749.156 Da / 分子数: 16 / 由来タイプ: 天然 由来: (天然) Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: Q7KLI1 #2: タンパク質 | 分子量: 51207.145 Da / 分子数: 16 / 由来タイプ: 天然 由来: (天然) Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: Q9XYF4, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ #3: 化合物 | ChemComp-ADP / |
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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 |
-試料調製
構成要素 |
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分子量 | 値: 3 MDa / 実験値: NO | ||||||||||||||||
緩衝液 | 名称: 25 mM Tris, pH 8.0, 150 mM NaCl, 5 mM DTT / pH: 8 / 詳細: 25 mM Tris, pH 8.0, 150 mM NaCl, 5 mM DTT | ||||||||||||||||
試料 | 濃度: 0.15 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: glow-discharged holey carbon grids (Quantifoil CuR2/2) with home-made continuous carbon film | ||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK II / 凍結剤: ETHANE / Temp: 85 K / 湿度: 100 % 詳細: Blot for 2 seconds before plunging into liquid ethane (FEI VITROBOT MARK II). 手法: Blot for 2 seconds before plunging |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI POLARA 300 / 日付: 2014年1月8日 |
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 FIELD / 倍率(公称値): 78000 X / 倍率(補正後): 104748 X / 最大 デフォーカス(公称値): 6400 nm / 最小 デフォーカス(公称値): 1400 nm / Cs: 2 mm |
試料ホルダ | 試料ホルダーモデル: GATAN LIQUID NITROGEN / 温度: 85 K / 最高温度: 90 K / 最低温度: 80 K |
撮影 | 電子線照射量: 28 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
画像スキャン | デジタル画像の数: 1234 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: Each particle | ||||||||||||
対称性 | 点対称性: D8 (2回x8回 2面回転対称) | ||||||||||||
3次元再構成 | 解像度: 4.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 11359 / ピクセルサイズ(公称値): 1.34 Å / ピクセルサイズ(実測値): 1.34 Å 詳細: To correct for beam-induced movements, the 16 video frames for each micrograph were first aligned using whole-image motion correction. Then particle-based beam-induced movement correction was ...詳細: To correct for beam-induced movements, the 16 video frames for each micrograph were first aligned using whole-image motion correction. Then particle-based beam-induced movement correction was performed using statistical movie processing in RELION. 対称性のタイプ: POINT | ||||||||||||
精密化ステップ | サイクル: LAST
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