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基本情報
登録情報 | データベース: PDB / ID: 1i3o | ||||||
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タイトル | CRYSTAL STRUCTURE OF THE COMPLEX OF XIAP-BIR2 AND CASPASE 3 | ||||||
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![]() | APOPTOSIS / complex / IAP / caspase | ||||||
機能・相同性 | ![]() regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / intrinsic apoptotic signaling pathway in response to osmotic stress ...regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / intrinsic apoptotic signaling pathway in response to osmotic stress / nucleotide-binding oligomerization domain containing 1 signaling pathway / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis / response to cobalt ion / cellular response to staurosporine / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / Apoptosis induced DNA fragmentation / Apoptotic cleavage of cell adhesion proteins / nucleotide-binding oligomerization domain containing 2 signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand / SMAC, XIAP-regulated apoptotic response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / death receptor binding / axonal fasciculation / regulation of synaptic vesicle cycle / fibroblast apoptotic process / epithelial cell apoptotic process / TNFR1-induced proapoptotic signaling / platelet formation / negative regulation of cytokine production / RIPK1-mediated regulated necrosis / Other interleukin signaling / response to anesthetic / execution phase of apoptosis / positive regulation of amyloid-beta formation / regulation of innate immune response / negative regulation of B cell proliferation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / neurotrophin TRK receptor signaling pathway / negative regulation of activated T cell proliferation / T cell homeostasis / response to tumor necrosis factor / negative regulation of cell cycle / B cell homeostasis / cysteine-type endopeptidase inhibitor activity / protein K63-linked ubiquitination / cell fate commitment / negative regulation of tumor necrosis factor-mediated signaling pathway / response to X-ray / positive regulation of type I interferon production / regulation of macroautophagy / Pyroptosis / Caspase-mediated cleavage of cytoskeletal proteins / response to amino acid / response to glucose / response to glucocorticoid / response to UV / keratinocyte differentiation / Degradation of the extracellular matrix / striated muscle cell differentiation / intrinsic apoptotic signaling pathway / protein serine/threonine kinase binding / Regulation of PTEN localization / protein maturation / hippocampus development / positive regulation of protein ubiquitination / erythrocyte differentiation / TNFR1-induced NF-kappa-B signaling pathway / response to nicotine / positive regulation of JNK cascade / Deactivation of the beta-catenin transactivating complex / enzyme activator activity / apoptotic signaling pathway / Regulation of TNFR1 signaling / response to hydrogen peroxide / sensory perception of sound / protein catabolic process / RING-type E3 ubiquitin transferase / regulation of protein stability / protein processing / Regulation of necroptotic cell death / response to wounding / Wnt signaling pathway / Regulation of PTEN stability and activity / neuron differentiation / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of neuron apoptotic process / positive regulation of canonical Wnt signaling pathway / response to estradiol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Riedl, S.J. / Renatus, M. / Schwarzenbacher, R. / Zhou, Q. / Sun, C. / Fesik, S.W. / Liddington, R.C. / Salvesen, G.S. | ||||||
![]() | ![]() タイトル: Structural basis for the inhibition of caspase-3 by XIAP. 著者: Riedl, S.J. / Renatus, M. / Schwarzenbacher, R. / Zhou, Q. / Sun, C. / Fesik, S.W. / Liddington, R.C. / Salvesen, G.S. | ||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDB形式 | ![]() | 117.8 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 409 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 430.3 KB | 表示 | |
XML形式データ | ![]() | 17.3 KB | 表示 | |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 19727.279 Da / 分子数: 2 / 断片: APOPAIN P17 SUBUNIT / 変異: C285A / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: P42574, 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 #2: タンパク質 | 分子量: 12981.756 Da / 分子数: 2 / 断片: APOPAIN P12 SUBUNIT / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: P42574, 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: タンパク質 | 分子量: 13993.578 Da / 分子数: 2 / 断片: XIAP-BIR2 / 変異: C202A, C213G / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #4: 化合物 | #5: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.61 Å3/Da / 溶媒含有率: 60.14 % | ||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.2 詳細: sodium formate, sodium acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 23 ℃ / pH: 7.6 | ||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 2000年12月15日 |
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 | 波長: 1.08 Å / 相対比: 1 |
反射 | 解像度: 2.7→500 Å / Num. all: 174633 / Num. obs: 27119 / % possible obs: 99.4 % / 冗長度: 5 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.062 |
反射 シェル | 解像度: 2.7→2.8 Å / 冗長度: 4.5 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2649 / % possible all: 99.3 |
反射 | *PLUS 最低解像度: 500 Å / Num. measured all: 174633 |
反射 シェル | *PLUS % possible obs: 99.3 % |
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解析
ソフトウェア |
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精密化 | 開始モデル: PDB ENTRY 1PAU and PDB ENTRY 1C9Q 解像度: 2.7→500 Å / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber / 詳細: MLF
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溶媒の処理 | 溶媒モデル: CNS BULK SOLVENT / Bsol: 33.0707 Å2 / ksol: 0.321299 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 29.938 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.7→500 Å
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拘束条件 |
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Xplor file |
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ソフトウェア | *PLUS 名称: CNS / バージョン: 1 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 2.7 Å / 最低解像度: 500 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.248 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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