+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1k3a | ||||||
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タイトル | Structure of the Insulin-like Growth Factor 1 Receptor Kinase | ||||||
要素 |
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キーワード | TRANSFERASE (転移酵素) / protein kinase (プロテインキナーゼ) / tyrosine kinase (プロテインチロシンキナーゼ) / tyrosine phosphorylation / protein-substrate complex | ||||||
機能・相同性 | 機能・相同性情報 cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / protein kinase complex / protein transporter activity / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / negative regulation of muscle cell apoptotic process ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / protein kinase complex / protein transporter activity / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / cellular response to zinc ion starvation / cellular response to aldosterone / IRS-mediated signalling / positive regulation of fatty acid beta-oxidation / insulin receptor complex / negative regulation of hepatocyte apoptotic process / cellular response to testosterone stimulus / insulin-like growth factor I binding / positive regulation of glucose metabolic process / insulin receptor activity / transcytosis / Activated NTRK3 signals through PI3K / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / transmembrane receptor protein tyrosine kinase adaptor activity / positive regulation of protein-containing complex disassembly / Signaling by Leptin / cellular response to angiotensin / PI3K/AKT activation / cellular response to insulin-like growth factor stimulus / response to L-glutamate / dendritic spine maintenance / cellular response to fatty acid / insulin binding / Signaling by ALK / establishment of cell polarity / negative regulation of MAPK cascade / IRS activation / positive regulation of axon regeneration / amyloid-beta clearance / positive regulation of cytokinesis / positive regulation of osteoblast proliferation / regulation of JNK cascade / estrous cycle / Signaling by ALK fusions and activated point mutants / SOS-mediated signalling / insulin receptor substrate binding / PI3K Cascade / G-protein alpha-subunit binding / negative regulation of insulin secretion / response to vitamin E / positive regulation of glycogen biosynthetic process / SHC-related events triggered by IGF1R / Signal attenuation / phosphatidylinositol 3-kinase binding / Growth hormone receptor signaling / positive regulation of insulin receptor signaling pathway / peptidyl-tyrosine autophosphorylation / negative regulation of insulin receptor signaling pathway / cellular response to transforming growth factor beta stimulus / 横行小管 / insulin-like growth factor receptor binding / Interleukin-7 signaling / SH2 domain binding / cerebellum development / phosphotyrosine residue binding / cellular response to dexamethasone stimulus / 軸索誘導 / protein kinase C binding / insulin-like growth factor receptor signaling pathway / response to nicotine / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to estradiol stimulus / カベオラ / hippocampus development / cellular response to glucose stimulus / positive regulation of glucose import / positive regulation of smooth muscle cell proliferation / response to insulin / insulin receptor binding / 受容体型チロシンキナーゼ / cytokine-mediated signaling pathway / cellular response to mechanical stimulus / cellular response to insulin stimulus / cellular response to amyloid-beta / Constitutive Signaling by Aberrant PI3K in Cancer / 細胞老化 / signaling receptor complex adaptor activity / glucose homeostasis / PIP3 activates AKT signaling / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / response to ethanol / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.1 Å | ||||||
データ登録者 | Favelyukis, S. / Till, J.H. / Hubbard, S.R. / Miller, W.T. | ||||||
引用 | ジャーナル: Nat.Struct.Biol. / 年: 2001 タイトル: Structure and autoregulation of the insulin-like growth factor 1 receptor kinase. 著者: Favelyukis, S. / Till, J.H. / Hubbard, S.R. / Miller, W.T. | ||||||
履歴 |
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Remark 999 | SEQUENCE THE RESIDUE CORRESPONDS TO RESIDUE FROM A SYNTHETIC PEPTIDE. IT WAS ADDED TO MODIFY THE ...SEQUENCE THE RESIDUE CORRESPONDS TO RESIDUE FROM A SYNTHETIC PEPTIDE. IT WAS ADDED TO MODIFY THE SEQUENCE TO BE SUITABLE FOR ACTIVITY ASSAYS |
-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 | 1k3a.cif.gz | 78.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1k3a.ent.gz | 56.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1k3a.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/k3/1k3a ftp://data.pdbj.org/pub/pdb/validation_reports/k3/1k3a | HTTPS FTP |
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-関連構造データ
関連構造データ | 1ir3S S: 精密化の開始モデル |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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単位格子 |
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詳細 | tetramer of 2 alpha and 2 beta chains linked by disulfide bonds. |
-要素
#1: タンパク質 | 分子量: 34410.199 Da / 分子数: 1 / 断片: beta chain, kinase domain (residues 988-1286) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pFast-Bac 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 株 (発現宿主): Sf9 / 参照: UniProt: P08069, EC: 2.7.1.112 |
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#2: タンパク質・ペプチド | 分子量: 1598.818 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: Chemically synthesized / 参照: UniProt: P35568 |
#3: 化合物 | ChemComp-ACP / |
#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: 2.9 Å3/Da / 溶媒含有率: 57.55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: PEG 8000, sodium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: シンクロトロン / サイト: NSLS / ビームライン: X4A / 波長: 0.9725 Å |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2001年5月22日 |
放射 | モノクロメーター: silicon crystal / 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: 0.9725 Å / 相対比: 1 |
反射 | 解像度: 2.1→28.07 Å / Num. all: 24941 / Num. obs: 24941 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.048 |
反射 シェル | 解像度: 2.1→2.18 Å / Rsym value: 0.254 / % possible all: 100 |
反射 | *PLUS 最低解像度: 25 Å / Num. measured all: 279673 / Rmerge(I) obs: 0.048 |
反射 シェル | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.254 |
-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: 1ir3 解像度: 2.1→28.07 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 387254.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 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: 46.8196 Å2 / ksol: 0.357892 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 33.9 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: 2.1→28.07 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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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 最低解像度: 25 Å / σ(F): 0 / % reflection Rfree: 9.8 % / Rfactor Rfree: 0.248 | ||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 33.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.275 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.231 |