+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5wve | ||||||||||||
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タイトル | Apaf-1-Caspase-9 holoenzyme | ||||||||||||
要素 |
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キーワード | APOPTOSIS / apoptosis holoenzyme | ||||||||||||
機能・相同性 | 機能・相同性情報 caspase-9 / response to G1 DNA damage checkpoint signaling / caspase complex / cytochrome c-heme linkage / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / cytochrome complex / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process ...caspase-9 / response to G1 DNA damage checkpoint signaling / caspase complex / cytochrome c-heme linkage / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / cytochrome complex / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of cysteine-type endopeptidase activity / Caspase activation via Dependence Receptors in the absence of ligand / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / AKT phosphorylates targets in the cytosol / mitochondrial electron transport, cytochrome c to oxygen / fibroblast apoptotic process / epithelial cell apoptotic process / platelet formation / mitochondrial electron transport, ubiquinol to cytochrome c / TP53 Regulates Transcription of Caspase Activators and Caspases / Transcriptional Regulation by E2F6 / Constitutive Signaling by AKT1 E17K in Cancer / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein maturation / : / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / signal transduction in response to DNA damage / forebrain development / cardiac muscle cell apoptotic process / enzyme activator activity / cellular response to transforming growth factor beta stimulus / heat shock protein binding / intrinsic apoptotic signaling pathway / cellular response to dexamethasone stimulus / response to nutrient / kidney development / neural tube closure / response to ischemia / positive regulation of apoptotic signaling pathway / NOD1/2 Signaling Pathway / mitochondrial intermembrane space / protein processing / ADP binding / SH3 domain binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / positive regulation of neuron apoptotic process / response to estradiol / nervous system development / peptidase activity / regulation of apoptotic process / secretory granule lumen / neuron apoptotic process / ficolin-1-rich granule lumen / response to lipopolysaccharide / electron transfer activity / cell differentiation / response to hypoxia / positive regulation of apoptotic process / cysteine-type endopeptidase activity / nucleotide binding / lipid binding / apoptotic process / DNA damage response / heme binding / Neutrophil degranulation / protein kinase binding / protein-containing complex / mitochondrion / proteolysis / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) Equus caballus (ウマ) | ||||||||||||
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: 4.4 Å | ||||||||||||
データ登録者 | Li, Y. / Zhou, M. / Hu, Q. / Shi, Y. | ||||||||||||
資金援助 | 中国, 英国, 3件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2017 タイトル: Mechanistic insights into caspase-9 activation by the structure of the apoptosome holoenzyme. 著者: Yini Li / Mengying Zhou / Qi Hu / Xiao-Chen Bai / Weiyun Huang / Sjors H W Scheres / Yigong Shi / 要旨: Mammalian intrinsic apoptosis requires activation of the initiator caspase-9, which then cleaves and activates the effector caspases to execute cell killing. The heptameric Apaf-1 apoptosome is ...Mammalian intrinsic apoptosis requires activation of the initiator caspase-9, which then cleaves and activates the effector caspases to execute cell killing. The heptameric Apaf-1 apoptosome is indispensable for caspase-9 activation by together forming a holoenzyme. The molecular mechanism of caspase-9 activation remains largely enigmatic. Here, we report the cryoelectron microscopy (cryo-EM) structure of an apoptotic holoenzyme and structure-guided biochemical analyses. The caspase recruitment domains (CARDs) of Apaf-1 and caspase-9 assemble in two different ways: a 4:4 complex docks onto the central hub of the apoptosome, and a 2:1 complex binds the periphery of the central hub. The interface between the CARD complex and the central hub is required for caspase-9 activation within the holoenzyme. Unexpectedly, the CARD of free caspase-9 strongly inhibits its proteolytic activity. These structural and biochemical findings demonstrate that the apoptosome activates caspase-9 at least in part through sequestration of the inhibitory CARD domain. | ||||||||||||
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 | 5wve.cif.gz | 1.7 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5wve.ent.gz | 1.4 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5wve.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 | 5wve_validation.pdf.gz | 2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5wve_full_validation.pdf.gz | 3 MB | 表示 | |
XML形式データ | 5wve_validation.xml.gz | 377 KB | 表示 | |
CIF形式データ | 5wve_validation.cif.gz | 530.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/wv/5wve ftp://data.pdbj.org/pub/pdb/validation_reports/wv/5wve | 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
-Apoptotic protease-activating factor ... , 2種, 13分子 ACEGIKMOPQRWX
#1: タンパク質 | 分子量: 142023.672 Da / 分子数: 7 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: APAF1, KIAA0413 発現宿主: Insect cell expression vector pTIE1 (その他) 参照: UniProt: O14727 #3: タンパク質 | 分子量: 11575.185 Da / 分子数: 6 / Fragment: CARD domain, UNP residues 1-102 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: APAF1, KIAA0413 発現宿主: Insect cell expression vector pTIE1 (その他) 参照: UniProt: O14727 |
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-タンパク質 , 2種, 12分子 BDFHJLNSTUVY
#2: タンパク質 | 分子量: 11856.793 Da / 分子数: 7 / 由来タイプ: 組換発現 / 由来: (組換発現) Equus caballus (ウマ) / 遺伝子: CYCS, CYC / 発現宿主: Bacteria (unknown) / 参照: UniProt: P00004 #4: タンパク質 | 分子量: 11698.449 Da / 分子数: 5 / Fragment: CARD domain, UNP residues 1-100 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Bacteria (unknown) / 参照: UniProt: A8K7U6, UniProt: P55211*PLUS |
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-非ポリマー , 3種, 21分子
#5: 化合物 | ChemComp-DTP / #6: 化合物 | ChemComp-MG / #7: 化合物 | ChemComp-HEM / |
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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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由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.5 | ||||||||||||||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE |
-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 |
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 |
撮影 | 電子線照射量: 32 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
-解析
CTF補正 | タイプ: NONE |
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3次元再構成 | 解像度: 4.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 240130 / 対称性のタイプ: POINT |