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基本情報
登録情報 | データベース: EMDB / ID: EMD-5186 | |||||||||
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タイトル | Structure of an apoptosome-procaspase-9 CARD complex | |||||||||
![]() | Structure of the human apoptosome with procaspase-9 CARD | |||||||||
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![]() | apoptosome / Apaf-1 / procaspase-9 CARD / apoptosis | |||||||||
機能・相同性 | ![]() Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / response to G1 DNA damage checkpoint signaling / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Formation of apoptosome / regulation of apoptotic DNA fragmentation ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / response to G1 DNA damage checkpoint signaling / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Formation of apoptosome / regulation of apoptotic DNA fragmentation / Detoxification of Reactive Oxygen Species / apoptosome / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / Respiratory electron transport / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / TP53 Regulates Transcription of Caspase Activators and Caspases / Transcriptional Regulation by E2F6 / cysteine-type endopeptidase activator activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / : / response to nutrient / forebrain development / cardiac muscle cell apoptotic process / cellular response to transforming growth factor beta stimulus / heat shock protein binding / intrinsic apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / kidney development / neural tube closure / mitochondrial intermembrane space / activation of cysteine-type endopeptidase activity involved in apoptotic process / ADP binding / nervous system development / secretory granule lumen / neuron apoptotic process / regulation of apoptotic process / ficolin-1-rich granule lumen / cell differentiation / response to hypoxia / electron transfer activity / positive regulation of apoptotic process / nucleotide binding / heme binding / Neutrophil degranulation / apoptotic process / protein-containing complex / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / 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: 9.5 Å | |||||||||
![]() | Yuan S / Yu X / Topf M / Ludtke SJ / Wang X / Akey CW | |||||||||
![]() | ![]() タイトル: Structure of an apoptosome-procaspase-9 CARD complex. 著者: Shujun Yuan / Xinchao Yu / Maya Topf / Steven J Ludtke / Xiaodong Wang / Christopher W Akey / ![]() 要旨: Apaf-1 coassembles with cytochrome c to form the apoptosome, which then binds and activates procaspase-9 (pc-9). We removed pc-9 catalytic domains from the holoapoptosome by site-directed ...Apaf-1 coassembles with cytochrome c to form the apoptosome, which then binds and activates procaspase-9 (pc-9). We removed pc-9 catalytic domains from the holoapoptosome by site-directed thrombinolysis. A structure of the resulting apoptosome-pc-9 CARD complex was then determined at approximately 9.5 A resolution. In our model, the central hub is constructed like other AAA+ protein rings but also contains novel features. At higher radius, the regulatory region of each Apaf-1 is comprised of tandem seven and eight blade beta-propellers with cytochrome c docked between them. Remarkably, Apaf-1 CARDs are disordered in the ground state. During activation, each Apaf-1 CARD interacts with a pc-9 CARD and these heterodimers form a flexibly tethered "disk" that sits above the central hub. When taken together, the data reveal conformational changes during Apaf-1 assembly that allow pc-9 activation. The model also provides a plausible explanation for the effects of NOD mutations that have been mapped onto the central hub. | |||||||||
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: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
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マップデータ | ![]() | 2.4 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 16.4 KB 16.4 KB | 表示 表示 | ![]() |
画像 | ![]() | 202.5 KB | ||
マスクデータ | ![]() | 30.5 MB | ![]() | |
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
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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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Structure of the human apoptosome with procaspase-9 CARD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.26 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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-添付データ
-セグメンテーションマップ: This is a mask used to filter the final 3D volume
注釈 | This is a mask used to filter the final 3D volume | ||||||||||||
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ファイル | ![]() | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
-全体 : human apoptosome with bound procaspase-9 CARD
全体 | 名称: human apoptosome with bound procaspase-9 CARD |
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要素 |
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-超分子 #1000: human apoptosome with bound procaspase-9 CARD
超分子 | 名称: human apoptosome with bound procaspase-9 CARD / タイプ: sample / ID: 1000 詳細: Apoptosomes were assembled in low salt buffer, procaspase-9 with a thrombin site in the CARD-p20 linker was added, and then the complex was thrombinized to release pc-9 catalytic domains. 集合状態: heptameric Apaf-1 in the apoptosome with 7 bound procaspase-9 CARDs Number unique components: 3 |
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分子量 | 理論値: 1.1 MDa |
-分子 #1: Apaf-1
分子 | 名称: Apaf-1 / タイプ: protein_or_peptide / ID: 1 / Name.synonym: Apaf-1 詳細: Seven Apaf-1 molecules were assembled with cytochrome c and dATP to form an apoptosome complex. 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 | 理論値: 135 KDa |
組換発現 | 生物種: sf21 insect cells (unknown) / 組換プラスミド: pFastBac1 |
配列 | GO: activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c InterPro: Apoptotic protease-activating factor 1 |
-分子 #2: procaspase-9
分子 | 名称: procaspase-9 / タイプ: protein_or_peptide / ID: 2 / Name.synonym: procaspase-9 詳細: procaspase-9 binds on the human apoptosome through CARD-CARD interactions. Procaspase-9 was added to the apoptosome in slight excess and then thrombinized to remove the catalytic domains. 組換発現: Yes |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 10 KDa |
組換発現 | 生物種: ![]() ![]() |
-分子 #3: cytochrome c
分子 | 名称: cytochrome c / タイプ: protein_or_peptide / ID: 3 / Name.synonym: cytochrome c / 詳細: cytochrome c is the assembly activator for Apaf-1 / コピー数: 7 / 集合状態: monomer / 組換発現: No / データベース: NCBI |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 10 KDa |
-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 | 3 mg/mL |
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緩衝液 | pH: 7.5 詳細: 20mM HEPES, 10mM KCl, 1.5mM MgCl2, 1mM EDTA, 1mM EGTA, 1mM DTT |
グリッド | 詳細: Quantifoil R1.2/1.3 holey grids |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 77 K / 装置: FEI VITROBOT MARK III / 詳細: Vitrification instrument: Vitrobot Mark 3 (FEI) / 手法: Blot for 2-3 seconds before plunging at 20C |
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電子顕微鏡法
顕微鏡 | FEI TECNAI F20 |
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温度 | 平均: 96 K |
アライメント法 | Legacy - 非点収差: objective lens astigmatism was corrected at 200,000 times magnification |
日付 | 2008年8月1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: ZEISS SCAI / デジタル化 - サンプリング間隔: 7 µm / 実像数: 400 / 平均電子線量: 25 e/Å2 / Od range: 1 |
電子線 | 加速電圧: 120 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 62000 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2 mm / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 1.5 µm / 倍率(公称値): 62000 |
試料ステージ | 試料ホルダー: Side entry liquid nitrogen-cooled cryo specimen holder. 試料ホルダーモデル: GATAN LIQUID NITROGEN |
実験機器 | ![]() モデル: Tecnai F20 / 画像提供: FEI Company |
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画像解析
詳細 | particles were selected with boxer |
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CTF補正 | 詳細: Each image |
最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 9.5 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: EMAN 詳細: Final map contains 34000 particles. Setsf filtration was applied to the final map to boost amplitude at high resolution range and in the last cycles of refinement. 使用した粒子像数: 42000 |
最終 2次元分類 | クラス数: 592 |
-原子モデル構築 1
初期モデル | PDB ID: Chain - Chain ID: A |
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ソフトウェア | 名称: ![]() |
詳細 | PDBEntryID_givenInChain. Protocol: rigid body for each domain. After chimera fitting, Flex-EM was used to improve fitting and minimize collisions. The beta propellers were modeled using the map as a restraint, sequence alignments and the crystal structure of actin interacting protein 1. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: cross correlation |
得られたモデル | ![]() PDB-3j2t: |