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基本情報
登録情報 | データベース: PDB / ID: 6vwj | |||||||||
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タイトル | Leg region of the closed conformation of the human type 1 insulin-like growth factor receptor ectodomain in complex with human insulin-like growth factor II | |||||||||
![]() | Leucine-zippered human type 1 insulin-like growth factor receptor ectodomain | |||||||||
![]() | SIGNALING PROTEIN / Type 1 insulin-like growth factor receptor / Insulin-like growth factor II / ectodomain receptor / tyrosine kinase | |||||||||
機能・相同性 | ![]() 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 / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / protein transporter activity / 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 / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / protein transporter activity / 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 / protein localization to nuclear periphery / FCERI mediated MAPK activation / cellular response to zinc ion starvation / cellular response to aldosterone / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / insulin receptor complex / cellular response to testosterone stimulus / negative regulation of hepatocyte apoptotic process / insulin-like growth factor I binding / insulin receptor activity / transcytosis / nitrogen catabolite activation of transcription from RNA polymerase II promoter / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / Respiratory syncytial virus (RSV) attachment and entry / Oxidative Stress Induced Senescence / positive regulation of protein-containing complex disassembly / cellular response to angiotensin / dendritic spine maintenance / cellular response to insulin-like growth factor stimulus / response to L-glutamate / insulin binding / negative regulation of MAPK cascade / establishment of cell polarity / positive regulation of axon regeneration / amyloid-beta clearance / positive regulation of osteoblast proliferation / positive regulation of cytokinesis / TFIID-class transcription factor complex binding / regulation of JNK cascade / insulin receptor substrate binding / estrous cycle / G-protein alpha-subunit binding / response to vitamin E / positive regulation of transcription initiation by RNA polymerase II / SHC-related events triggered by IGF1R / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / phosphatidylinositol 3-kinase binding / peptidyl-tyrosine autophosphorylation / cellular response to transforming growth factor beta stimulus / T-tubule / cellular response to amino acid starvation / cerebellum development / cellular response to dexamethasone stimulus / axonogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / insulin-like growth factor receptor signaling pathway / caveola / cellular response to estradiol stimulus / hippocampus development / cellular response to glucose stimulus / positive regulation of smooth muscle cell proliferation / response to nicotine / insulin receptor binding / receptor protein-tyrosine kinase / cellular response to mechanical stimulus / RNA polymerase II transcription regulator complex / cellular response to amyloid-beta / : / cellular senescence / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / protein tyrosine kinase activity / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / positive regulation of MAPK cascade / protein autophosphorylation / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / positive regulation of cell migration / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / axon / intracellular membrane-bounded organelle / neuronal cell body 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() | |||||||||
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: 4.21 Å | |||||||||
![]() | Xu, Y. / Kirk, N.S. / Lawrence, M.C. / Croll, T.I. | |||||||||
資金援助 | ![]() ![]()
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![]() | ![]() タイトル: How IGF-II Binds to the Human Type 1 Insulin-like Growth Factor Receptor. 著者: Yibin Xu / Nicholas S Kirk / Hariprasad Venugopal / Mai B Margetts / Tristan I Croll / Jarrod J Sandow / Andrew I Webb / Carlie A Delaine / Briony E Forbes / Michael C Lawrence / ![]() ![]() 要旨: Human type 1 insulin-like growth factor receptor (IGF-1R) signals chiefly in response to the binding of insulin-like growth factor I. Relatively little is known about the role of insulin-like growth ...Human type 1 insulin-like growth factor receptor (IGF-1R) signals chiefly in response to the binding of insulin-like growth factor I. Relatively little is known about the role of insulin-like growth factor II signaling via IGF-1R, despite the affinity of insulin-like growth factor II for IGF-1R being within an order of magnitude of that of insulin-like growth factor I. Here, we describe the cryoelectron microscopy structure of insulin-like growth factor II bound to a leucine-zipper-stabilized IGF-1R ectodomain, determined in two conformations to a maximum average resolution of 3.2 Å. The two conformations differ in the relative separation of their respective points of membrane entry, and comparison with the structure of insulin-like growth factor I bound to IGF-1R reveals long-suspected differences in the way in which the critical C domain of the respective growth factors interact with IGF-1R. | |||||||||
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構造の表示
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 275.2 KB | 表示 | ![]() |
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PDB形式 | ![]() | 219.5 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 780.6 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 789 KB | 表示 | |
XML形式データ | ![]() | 28.2 KB | 表示 | |
CIF形式データ | ![]() | 40.7 KB | 表示 | |
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
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質 | 分子量: 108937.242 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() ![]() 遺伝子: IGF1R, GCN4, AAS3, ARG9, YEL009C / プラスミド: pEE14 / 株: ATCC 204508 / S288c / 細胞株 (発現宿主): CHO-K1 発現宿主: ![]() ![]() 参照: UniProt: P08069, UniProt: P03069, receptor protein-tyrosine kinase |
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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 |
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試料調製
構成要素 | 名称: Leg region of the open-leg conformation of the human type 1 insulin-like growth factor receptor ectodomain in complex with human insulin-like growth factor II タイプ: COMPLEX / Entity ID: all / 由来: MULTIPLE SOURCES | ||||||||||||||||||||
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分子量 | 値: 0.25 MDa / 実験値: NO | ||||||||||||||||||||
由来(天然) | 生物種: ![]() | ||||||||||||||||||||
由来(組換発現) | 生物種: ![]() ![]() | ||||||||||||||||||||
緩衝液 | pH: 7.5 | ||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: IGFII:IGF-1R molar ratio 1.5:1 | ||||||||||||||||||||
試料支持 | 詳細: 15mA current / グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil, UltrAuFoil, R1.2/1.3 | ||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / Cs: 2.7 mm / C2レンズ絞り径: 50 µm |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 平均露光時間: 10 sec. / 電子線照射量: 50 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 撮影したグリッド数: 1 / 実像数: 4585 |
電子光学装置 | エネルギーフィルター名称: GIF Quantum LS |
画像スキャン | 動画フレーム数/画像: 50 / 利用したフレーム数/画像: 1-50 |
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解析
ソフトウェア |
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 2057701 | ||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.21 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 108899 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL 詳細: UCSF Chimera was used for the initial fitting and ISOLDE v 1.03b was using for flexible fitting. | ||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 5U8R | ||||||||||||||||||||||||||||||||
精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 139.51 Å2 | ||||||||||||||||||||||||||||||||
拘束条件 |
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