+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6hn5 | |||||||||||||||
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タイトル | Leucine-zippered human insulin receptor ectodomain with single bound insulin - "upper" membrane-distal part | |||||||||||||||
要素 |
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キーワード | SIGNALING PROTEIN / insulin / insulin receptor ectodomain / signal transduction | |||||||||||||||
機能・相同性 | 機能・相同性情報 regulation of female gonad development / positive regulation of meiotic cell cycle / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / insulin-like growth factor II binding / positive regulation of developmental growth / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II ...regulation of female gonad development / positive regulation of meiotic cell cycle / protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / insulin-like growth factor II binding / positive regulation of developmental growth / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / positive regulation of protein-containing complex disassembly / cargo receptor activity / dendritic spine maintenance / insulin binding / PTB domain binding / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / adrenal gland development / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / activation of protein kinase activity / Insulin processing / neuronal cell body membrane / regulation of protein secretion / amyloid-beta clearance / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / positive regulation of receptor internalization / TFIID-class transcription factor complex binding / alpha-beta T cell activation / regulation of embryonic development / regulation of cellular amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / insulin receptor substrate binding / transport across blood-brain barrier / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Synthesis, secretion, and deacylation of Ghrelin / epidermis development / positive regulation of transcription initiation by RNA polymerase II / negative regulation of protein secretion / amino acid biosynthetic process / regulation of protein localization to plasma membrane / fatty acid homeostasis / cellular response to nutrient levels / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / phosphatidylinositol 3-kinase binding / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / heart morphogenesis / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / dendrite membrane / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / cellular response to amino acid starvation / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / receptor-mediated endocytosis / positive regulation of MAP kinase activity / positive regulation of nitric-oxide synthase activity / learning / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / caveola / acute-phase response / Regulation of insulin secretion / negative regulation of protein catabolic process / endosome lumen / positive regulation of glucose import / positive regulation of protein secretion / receptor protein-tyrosine kinase 類似検索 - 分子機能 | |||||||||||||||
生物種 | Homo sapiens (ヒト) Saccharomyces cerevisiae (パン酵母) | |||||||||||||||
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: 3.2 Å | |||||||||||||||
データ登録者 | Weis, F. / Menting, J.G. / Margetts, M.B. / Chan, S.J. / Xu, Y. / Tennagels, N. / Wohlfart, P. / Langer, T. / Mueller, C.W. / Dreyer, M.K. / Lawrence, M.C. | |||||||||||||||
資金援助 | オーストラリア, 米国, 4件
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引用 | ジャーナル: Nat Commun / 年: 2018 タイトル: The signalling conformation of the insulin receptor ectodomain. 著者: Felix Weis / John G Menting / Mai B Margetts / Shu Jin Chan / Yibin Xu / Norbert Tennagels / Paulus Wohlfart / Thomas Langer / Christoph W Müller / Matthias K Dreyer / Michael C Lawrence / 要旨: Understanding the structural biology of the insulin receptor and how it signals is of key importance in the development of insulin analogs to treat diabetes. We report here a cryo-electron microscopy ...Understanding the structural biology of the insulin receptor and how it signals is of key importance in the development of insulin analogs to treat diabetes. We report here a cryo-electron microscopy structure of a single insulin bound to a physiologically relevant, high-affinity version of the receptor ectodomain, the latter generated through attachment of C-terminal leucine zipper elements to overcome the conformational flexibility associated with ectodomain truncation. The resolution of the cryo-electron microscopy maps is 3.2 Å in the insulin-binding region and 4.2 Å in the membrane-proximal region. The structure reveals how the membrane proximal domains of the receptor come together to effect signalling and how insulin's negative cooperativity of binding likely arises. Our structure further provides insight into the high affinity of certain super-mitogenic insulins. Together, these findings provide a new platform for insulin analog investigation and design. | |||||||||||||||
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 | 6hn5.cif.gz | 197.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6hn5.ent.gz | 155.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6hn5.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 | 6hn5_validation.pdf.gz | 804.4 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6hn5_full_validation.pdf.gz | 816.5 KB | 表示 | |
XML形式データ | 6hn5_validation.xml.gz | 33.8 KB | 表示 | |
CIF形式データ | 6hn5_validation.cif.gz | 49.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/hn/6hn5 ftp://data.pdbj.org/pub/pdb/validation_reports/hn/6hn5 | 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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-要素
#1: タンパク質・ペプチド | 分子量: 2383.698 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P01308 | ||||
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#2: タンパク質・ペプチド | 分子量: 3433.953 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P01308 | ||||
#3: タンパク質 | 分子量: 106728.211 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Homo sapiens (ヒト), (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 遺伝子: INSR, GCN4, AAS3, ARG9, YEL009C / プラスミド: PEE14 / 株: ATCC 204508 / S288c / 細胞株 (発現宿主): Lec8 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 参照: UniProt: P06213, UniProt: P03069, receptor protein-tyrosine kinase #4: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #5: 糖 | ChemComp-NAG / |
-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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分子量 | 単位: MEGADALTONS / 実験値: NO | ||||||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.5 | ||||||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.094 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||
試料支持 | 詳細: PELCO easiGlow factory settings / グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: C-flat-2/2 | ||||||||||||||||||||||||||||
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: 283.15 K |
-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: 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 / 倍率(公称値): 130000 X / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 16 sec. / 電子線照射量: 1.85 e/Å2 / 検出モード: SUPER-RESOLUTION 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: 2287 |
電子光学装置 | エネルギーフィルター名称: GIF Quantum LS / エネルギーフィルタースリット幅: 20 eV |
画像スキャン | 動画フレーム数/画像: 20 / 利用したフレーム数/画像: 1-20 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.13-2998_1692: / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||
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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: 747074 | ||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 213867 / アルゴリズム: BACK PROJECTION / クラス平均像の数: 2 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 4ZXB |