+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3d9u | ||||||
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タイトル | The BIR3 domain of cIAP1 in complex with the N terminal peptide from SMAC/DIABLO (AVPIAQ). | ||||||
要素 |
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キーワード | APOPTOSIS (アポトーシス) / zinc finger (ジンクフィンガー) / Cytoplasm (細胞質) / Metal-binding / Polymorphism / Zinc (亜鉛) / Zinc-finger (ジンクフィンガー) | ||||||
機能・相同性 | 機能・相同性情報 negative regulation of ripoptosome assembly involved in necroptotic process / regulation of cysteine-type endopeptidase activity / FBXO family protein binding / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / Release of apoptotic factors from the mitochondria ...negative regulation of ripoptosome assembly involved in necroptotic process / regulation of cysteine-type endopeptidase activity / FBXO family protein binding / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / Release of apoptotic factors from the mitochondria / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of protein K63-linked ubiquitination / CD40 receptor complex / XY body / negative regulation of necroptotic process / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / regulation of reactive oxygen species metabolic process / positive regulation of protein monoubiquitination / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / intrinsic apoptotic signaling pathway in response to oxidative stress / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / non-canonical NF-kappaB signal transduction / necroptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / canonical NF-kappaB signal transduction / response to cAMP / tumor necrosis factor-mediated signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / intrinsic apoptotic signaling pathway / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / positive regulation of protein ubiquitination / TNFR2 non-canonical NF-kB pathway / placenta development / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / ミトコンドリア / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin protein ligase activity / regulation of cell population proliferation / protein-folding chaperone binding / regulation of inflammatory response / transferase activity / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / transcription coactivator activity / cell surface receptor signaling pathway / response to hypoxia / Ub-specific processing proteases / regulation of cell cycle / positive regulation of apoptotic process / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / ミトコンドリア / zinc ion binding / identical protein binding / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 2.3 Å | ||||||
データ登録者 | Kulathila, R. / Price, A. | ||||||
引用 | ジャーナル: Acta Crystallogr.,Sect.D / 年: 2009 タイトル: The structure of the BIR3 domain of cIAP1 in complex with the N-terminal peptides of SMAC and caspase-9. 著者: Kulathila, R. / Vash, B. / Sage, D. / Cornell-Kennon, S. / Wright, K. / Koehn, J. / Stams, T. / Clark, K. / Price, A. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 3d9u.cif.gz | 35.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3d9u.ent.gz | 23.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3d9u.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/d9/3d9u ftp://data.pdbj.org/pub/pdb/validation_reports/d9/3d9u | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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単位格子 |
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Components on special symmetry positions |
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詳細 | The biological unit is a heterodimeric complex of CIAP1-BIR3 with N-terminal peptide from SMAC/DIABLO (AVPIAQ). |
-要素
#1: タンパク質 | 分子量: 11174.601 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BIRC2, API1, IAP2, MIHB, RNF48 / プラスミド: pNAT40 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 DE3 / 参照: UniProt: Q13490 |
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#2: タンパク質・ペプチド | 分子量: 597.703 Da / 分子数: 1 / 由来タイプ: 合成 詳細: peptide synthesized based on N-terminal fragment of SMAC/DIABLO (AVPIAQ). 参照: UniProt: Q9NR28*PLUS |
#3: 化合物 | ChemComp-ZN / |
#4: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.8 Å3/Da / 溶媒含有率: 56.15 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: 0.1 M BIS-TRIS PH 6.5, 0.2 M MGCL2, 22% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: 回転陽極 / タイプ: RIGAKU FR-E DW / 波長: 1.54 Å |
検出器 | タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 2006年7月11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: 1.54 Å / 相対比: 1 |
反射 | 解像度: 2.3→54.6 Å / Num. all: 6497 / Num. obs: 6193 / % possible obs: 95.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / 冗長度: 15.7 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.191 / Net I/σ(I): 20.8 |
反射 シェル | 解像度: 2.3→2.38 Å / 冗長度: 15.6 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 4 / Num. unique all: 607 / % possible all: 96.8 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB entry 1NW9 解像度: 2.3→31.43 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 309778.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 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
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 38.1086 Å2 / ksol: 0.357278 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 31.3 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.3→31.43 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.3→2.44 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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