+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9838 | ||||||||||||
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タイトル | Cryo-EM structure of the full-length human IGF-1R in complex with insulin | ||||||||||||
マップデータ | |||||||||||||
試料 |
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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 / 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 / cellular response to zinc ion starvation / cellular response to aldosterone / insulin receptor complex / cellular response to testosterone stimulus / negative regulation of hepatocyte apoptotic process / insulin-like growth factor I binding / insulin receptor activity / transcytosis / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / cellular response to angiotensin / positive regulation of protein-containing complex disassembly / dendritic spine maintenance / cellular response to insulin-like growth factor stimulus / insulin binding / response to L-glutamate / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / negative regulation of MAPK cascade / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / establishment of cell polarity / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / positive regulation of axon regeneration / regulation of protein secretion / amyloid-beta clearance / positive regulation of osteoblast proliferation / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / positive regulation of cytokinesis / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / Respiratory syncytial virus (RSV) attachment and entry / alpha-beta T cell activation / regulation of JNK cascade / regulation of cellular amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / insulin receptor substrate binding / positive regulation of dendritic spine maintenance / estrous cycle / positive regulation of glycogen biosynthetic process / G-protein alpha-subunit binding / response to vitamin E / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / SHC-related events triggered by IGF1R / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / phosphatidylinositol 3-kinase binding / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / peptidyl-tyrosine autophosphorylation / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / cellular response to transforming growth factor beta stimulus / T-tubule / Insulin receptor recycling / neuron projection maintenance / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / cellular response to dexamethasone stimulus / cerebellum development / axonogenesis / insulin-like growth factor receptor signaling pathway / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / caveola / acute-phase response / cellular response to estradiol stimulus 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 5.0 Å | ||||||||||||
データ登録者 | Zhang X / Yu D / Wang T | ||||||||||||
資金援助 | 中国, 3件
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引用 | ジャーナル: Structure / 年: 2020 タイトル: Visualization of Ligand-Bound Ectodomain Assembly in the Full-Length Human IGF-1 Receptor by Cryo-EM Single-Particle Analysis. 著者: Xi Zhang / Daqi Yu / Jingchuan Sun / Yujie Wu / Junyuan Gong / Xuemei Li / Li Liu / Shan Liu / Jianbo Liu / Yulan Wu / Dongyang Li / Yinping Ma / Xu Han / Yanan Zhu / Zhaolong Wu / Yihua Wang ...著者: Xi Zhang / Daqi Yu / Jingchuan Sun / Yujie Wu / Junyuan Gong / Xuemei Li / Li Liu / Shan Liu / Jianbo Liu / Yulan Wu / Dongyang Li / Yinping Ma / Xu Han / Yanan Zhu / Zhaolong Wu / Yihua Wang / Qi Ouyang / Tao Wang / 要旨: Tyrosine kinase receptor of insulin-like growth factor 1 receptor (IGF-1R) and insulin receptor (IR) bind to hormones, such as insulin, IGF-1, and IGF-2, and transduces the signals across the cell ...Tyrosine kinase receptor of insulin-like growth factor 1 receptor (IGF-1R) and insulin receptor (IR) bind to hormones, such as insulin, IGF-1, and IGF-2, and transduces the signals across the cell membrane. However, the complete structure of the receptor and the signal transduction mechanism remains unclear. Here, we report the cryo-EM structure of the ligand-bound ectodomain in the full-length human IGF-1R. We reconstructed the IGF-1R/insulin complex at 4.7 Å and the IGF-1R/IGF-1 complex at 7.7 Å. Our structures reveal that only one insulin or one IGF-1 molecule binds to and activates the full-length human IGF-1R receptor. | ||||||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_9838.map.gz | 1.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9838-v30.xml emd-9838.xml | 15.1 KB 15.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_9838_fsc.xml | 5.8 KB | 表示 | FSCデータファイル |
画像 | emd_9838.png | 160.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9838 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9838 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_9838_validation.pdf.gz | 362.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_9838_full_validation.pdf.gz | 362.3 KB | 表示 | |
XML形式データ | emd_9838_validation.xml.gz | 8.5 KB | 表示 | |
CIF形式データ | emd_9838_validation.cif.gz | 10.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9838 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9838 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_9838.map.gz / 形式: CCP4 / 大きさ: 15.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : complex of full-length human type 1 insulin-like growth factor re...
全体 | 名称: complex of full-length human type 1 insulin-like growth factor receptor with insulin |
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要素 |
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-超分子 #1: complex of full-length human type 1 insulin-like growth factor re...
超分子 | 名称: complex of full-length human type 1 insulin-like growth factor receptor with insulin タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #2 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) / 組換細胞: HEK293T |
分子量 | 実験値: 310 KDa |
-分子 #1: Insulin-like growth factor 1 receptor
分子 | 名称: Insulin-like growth factor 1 receptor / タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO / EC番号: receptor protein-tyrosine kinase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 154.964469 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MKSGSGGGSP TSLWGLLFLS AALSLWPTSG EICGPGIDIR NDYQQLKRLE NCTVIEGYLH ILLISKAEDY RSYRFPKLTV ITEYLLLFR VAGLESLGDL FPNLTVIRGW KLFYNYALVI FEMTNLKDIG LYNLRNITRG AIRIEKNADL CYLSTVDWSL I LDAVSNNY ...文字列: MKSGSGGGSP TSLWGLLFLS AALSLWPTSG EICGPGIDIR NDYQQLKRLE NCTVIEGYLH ILLISKAEDY RSYRFPKLTV ITEYLLLFR VAGLESLGDL FPNLTVIRGW KLFYNYALVI FEMTNLKDIG LYNLRNITRG AIRIEKNADL CYLSTVDWSL I LDAVSNNY IVGNKPPKEC GDLCPGTMEE KPMCEKTTIN NEYNYRCWTT NRCQKMCPST CGKRACTENN ECCHPECLGS CS APDNDTA CVACRHYYYA GVCVPACPPN TYRFEGWRCV DRDFCANILS AESSDSEGFV IHDGECMQEC PSGFIRNGSQ SMY CIPCEG PCPKVCEEEK KTKTIDSVTS AQMLQGCTIF KGNLLINIRR GNNIASELEN FMGLIEVVTG YVKIRHSHAL VSLS FLKNL RLILGEEQLE GNYSFYVLDN QNLQQLWDWD HRNLTIKAGK MYFAFNPKLC VSEIYRMEEV TGTKGRQSKG DINTR NNGE RASCESDVLH FTSTTTSKNR IIITWHRYRP PDYRDLISFT VYYKEAPFKN VTEYDGQDAC GSNSWNMVDV DLPPNK DVE PGILLHGLKP WTQYAVYVKA VTLTMVENDH IRGAKSEILY IRTNASVPSI PLDVLSASNS SSQLIVKWNP PSLPNGN LS YYIVRWQRQP QDGYLYRHNY CSKDKIPIRK YADGTIDIEE VTENPKTEVC GGEKGPCCAC PKTEAEKQAE KEEAEYRK V FENFLHNSIF VPRPERKRRD VMQVANTTMS SRSRNTTAAD TYNITDPEEL ETEYPFFESR VDNKERTVIS NLRPFTLYR IDIHSCNHEA EKLGCSASNF VFARTMPAEG ADDIPGPVTW EPRPENSIFL KWPEPENPNG LILMYEIKYG SQVEDQRECV SRQEYRKYG GAKLNRLNPG NYTARIQATS LSGNGSWTDP VFFYVQAKTG YENFIHLIIA LPVAVLLIVG GLVIMLYVFH R KRNNSRLG NGVLYASVNP EYFSAADVYV PDEWEVAREK ITMSRELGQG SFGMVYEGVA KGVVKDEPET RVAIKTVNEA AS MRERIEF LNEASVMKEF NCHHVVRLLG VVSQGQPTLV IMELMTRGDL KSYLRSLRPE MENNPVLAPP SLSKMIQMAG EIA DGMAYL NANKFVHRDL AARNCMVAED FTVKIGDFGM TRDIYETDYY RKGGKGLLPV RWMSPESLKD GVFTTYSDVW SFGV VLWEI ATLAEQPYQG LSNEQVLRFV MEGGLLDKPD NCPDMLFELM RMCWQYNPKM RPSFLEIISS IKEEMEPGFR EVSFY YSEE NKLPEPEELD LEPENMESVP LDPSASSSSL PLPDRHSGHK AENGPGPGVL VLRASFDERQ PYAHMNGGRK NERALP LPQ SSTC |
-分子 #2: Insulin
分子 | 名称: Insulin / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 11.989862 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MALWMRLLPL LALLALWGPD PAAAFVNQHL CGSHLVEALY LVCGERGFFY TPKTRREAED LQVGQVELGG GPGAGSLQPL ALEGSLQKR GIVEQCCTSI CSLYQLENYC N |
-分子 #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
分子 | 名称: 2-acetamido-2-deoxy-beta-D-glucopyranose / タイプ: ligand / ID: 5 / コピー数: 6 / 式: NAG |
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分子量 | 理論値: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 2 mg/mL |
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緩衝液 | pH: 7.4 / 詳細: PBS with detergent |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: PLASMA CLEANING |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 278 K / 装置: FEI VITROBOT MARK IV |
詳細 | human type 1 insulin-like growth factor receptor saturated with human insulin |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 36496 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 倍率(公称値): 105000 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |