+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-41138 | |||||||||
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タイトル | CryoEM structure of MFRV-VILP bound to IGF1Rzip | |||||||||
マップデータ | Map of MFRV-VILP bound to IGFRzip, reconstructed using 3D flexible refinement | |||||||||
試料 |
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キーワード | IGF1R / MFRV-VILP / VILP / SIGNALING PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 cardiac atrium development / negative regulation of cholangiocyte apoptotic process / protein kinase complex / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / insulin-like growth factor binding / IRS-related events triggered by IGF1R / protein transporter activity / negative regulation of muscle cell apoptotic process ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / protein kinase complex / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / insulin-like growth factor binding / IRS-related events triggered by IGF1R / protein transporter activity / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / cellular response to aldosterone / cellular response to zinc ion starvation / insulin receptor complex / insulin-like growth factor I binding / cellular response to testosterone stimulus / negative regulation of hepatocyte apoptotic process / 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 / insulin binding / response to L-glutamate / cellular response to insulin-like growth factor stimulus / establishment of cell polarity / positive regulation of cytokinesis / positive regulation of axon regeneration / positive regulation of osteoblast proliferation / amyloid-beta clearance / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / insulin receptor substrate binding / response to vitamin E / G-protein alpha-subunit binding / estrous cycle / negative regulation of MAPK cascade / SHC-related events triggered by IGF1R / phosphatidylinositol 3-kinase binding / peptidyl-tyrosine autophosphorylation / cellular response to transforming growth factor beta stimulus / insulin-like growth factor receptor binding / T-tubule / phosphatidylinositol 3-kinase/protein kinase B signal transduction / axonogenesis / cellular response to dexamethasone stimulus / cerebellum development / insulin-like growth factor receptor signaling pathway / cellular response to estradiol stimulus / hippocampus development / response to nicotine / cellular response to glucose stimulus / positive regulation of smooth muscle cell proliferation / insulin receptor binding / regulation of protein phosphorylation / receptor protein-tyrosine kinase / caveola / hormone activity / cellular response to mechanical stimulus / cellular response to amyloid-beta / cellular senescence / positive regulation of cold-induced thermogenesis / insulin receptor signaling pathway / protein tyrosine kinase activity / response to ethanol / protein autophosphorylation / cell population proliferation / positive regulation of MAPK cascade / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration / immune response / axon / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / protein-containing complex binding / negative regulation of apoptotic process / signal transduction / extracellular space / ATP binding / identical protein binding / membrane / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | Mandarin fish ranavirus (ウイルス) / 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: 3.05 Å | |||||||||
データ登録者 | Kirk NS | |||||||||
資金援助 | チェコ, 2件
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引用 | ジャーナル: Mol Metab / 年: 2024 タイトル: A viral insulin-like peptide inhibits IGF-1 receptor phosphorylation and regulates IGF1R gene expression. 著者: Martina Chrudinová / Nicholas S Kirk / Aurelien Chuard / Hari Venugopal / Fa Zhang / Marta Lubos / Vasily Gelfanov / Terezie Páníková / Lenka Žáková / Julianne Cutone / Matthew Mojares ...著者: Martina Chrudinová / Nicholas S Kirk / Aurelien Chuard / Hari Venugopal / Fa Zhang / Marta Lubos / Vasily Gelfanov / Terezie Páníková / Lenka Žáková / Julianne Cutone / Matthew Mojares / Richard DiMarchi / Jiří Jiráček / Emrah Altindis / 要旨: OBJECTIVE: The insulin/IGF superfamily is conserved across vertebrates and invertebrates. Our team has identified five viruses containing genes encoding viral insulin/IGF-1 like peptides (VILPs) ...OBJECTIVE: The insulin/IGF superfamily is conserved across vertebrates and invertebrates. Our team has identified five viruses containing genes encoding viral insulin/IGF-1 like peptides (VILPs) closely resembling human insulin and IGF-1. This study aims to characterize the impact of Mandarin fish ranavirus (MFRV) and Lymphocystis disease virus-Sa (LCDV-Sa) VILPs on the insulin/IGF system for the first time. 手法: We chemically synthesized single chain (sc, IGF-1 like) and double chain (dc, insulin like) forms of MFRV and LCDV-Sa VILPs. Using cell lines overexpressing either human insulin receptor ...手法: We chemically synthesized single chain (sc, IGF-1 like) and double chain (dc, insulin like) forms of MFRV and LCDV-Sa VILPs. Using cell lines overexpressing either human insulin receptor isoform A (IR-A), isoform B (IR-B) or IGF-1 receptor (IGF1R), and AML12 murine hepatocytes, we characterized receptor binding, insulin/IGF signaling. We further characterized the VILPs' effects of proliferation and IGF1R and IR gene expression, and compared them to native ligands. Additionally, we performed insulin tolerance test in CB57BL/6 J mice to examine in vivo effects of VILPs on blood glucose levels. Finally, we employed cryo-electron microscopy (cryoEM) to analyze the structure of scMFRV-VILP in complex with the IGF1R ectodomain. RESULTS: VILPs can bind to human IR and IGF1R, stimulate receptor autophosphorylation and downstream signaling pathways. Notably, scMFRV-VILP exhibited a particularly strong affinity for IGF1R, with ...RESULTS: VILPs can bind to human IR and IGF1R, stimulate receptor autophosphorylation and downstream signaling pathways. Notably, scMFRV-VILP exhibited a particularly strong affinity for IGF1R, with a mere 10-fold decrease compared to human IGF-1. At high concentrations, scMFRV-VILP selectively reduced IGF-1 stimulated IGF1R autophosphorylation and Erk phosphorylation (Ras/MAPK pathway), while leaving Akt phosphorylation (PI3K/Akt pathway) unaffected, indicating a potential biased inhibitory function. Prolonged exposure to MFRV-VILP led to a significant decrease in IGF1R gene expression in IGF1R overexpressing cells and AML12 hepatocytes. Furthermore, insulin tolerance test revealed scMFRV-VILP's sustained glucose-lowering effect compared to insulin and IGF-1. Finally, cryo-EM analysis revealed that scMFRV-VILP engages with IGF1R in a manner closely resembling IGF-1 binding, resulting in a highly analogous structure. CONCLUSIONS: This study introduces MFRV and LCDV-Sa VILPs as novel members of the insulin/IGF superfamily. Particularly, scMFRV-VILP exhibits a biased inhibitory effect on IGF1R signaling at high ...CONCLUSIONS: This study introduces MFRV and LCDV-Sa VILPs as novel members of the insulin/IGF superfamily. Particularly, scMFRV-VILP exhibits a biased inhibitory effect on IGF1R signaling at high concentrations, selectively inhibiting IGF-1 stimulated IGF1R autophosphorylation and Erk phosphorylation, without affecting Akt phosphorylation. In addition, MFRV-VILP specifically regulates IGF-1R gene expression and IGF1R protein levels without affecting IR. CryoEM analysis confirms that scMFRV-VILP' binding to IGF1R is mirroring the interaction pattern observed with IGF-1. These findings offer valuable insights into IGF1R action and inhibition, suggesting potential applications in development of IGF1R specific inhibitors and advancing long-lasting insulins. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_41138.map.gz | 25.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-41138-v30.xml emd-41138.xml | 21.3 KB 21.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_41138_fsc.xml | 6.4 KB | 表示 | FSCデータファイル |
画像 | emd_41138.png | 73.4 KB | ||
マスクデータ | emd_41138_msk_1.map | 3.4 MB | マスクマップ | |
Filedesc metadata | emd-41138.cif.gz | 7 KB | ||
その他 | emd_41138_additional_1.map.gz emd_41138_half_map_1.map.gz emd_41138_half_map_2.map.gz | 1.7 MB 2 MB 2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-41138 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41138 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_41138_validation.pdf.gz | 601.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_41138_full_validation.pdf.gz | 601.4 KB | 表示 | |
XML形式データ | emd_41138_validation.xml.gz | 13.7 KB | 表示 | |
CIF形式データ | emd_41138_validation.cif.gz | 17.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41138 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41138 | HTTPS FTP |
-関連構造データ
関連構造データ | 8tanMC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_41138.map.gz / 形式: CCP4 / 大きさ: 27 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Map of MFRV-VILP bound to IGFRzip, reconstructed using 3D flexible refinement | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | emd_41138_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: DeepEMHancer-sharpened map of MFRV-VILP bound to IGFRzip, reconstructed...
ファイル | emd_41138_additional_1.map | ||||||||||||
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注釈 | DeepEMHancer-sharpened map of MFRV-VILP bound to IGFRzip, reconstructed using 3D flexible refinement | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half-map B of MFRV-VILP bound to IGFRzip, reconstructed...
ファイル | emd_41138_half_map_1.map | ||||||||||||
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注釈 | Half-map B of MFRV-VILP bound to IGFRzip, reconstructed using 3D flexible refinement | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half-map A of MFRV-VILP bound to IGFRzip, reconstructed...
ファイル | emd_41138_half_map_2.map | ||||||||||||
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注釈 | Half-map A of MFRV-VILP bound to IGFRzip, reconstructed using 3D flexible refinement | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : 1:2 complex of MFRV-VILP bound to IGF1Rzip
全体 | 名称: 1:2 complex of MFRV-VILP bound to IGF1Rzip |
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要素 |
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-超分子 #1: 1:2 complex of MFRV-VILP bound to IGF1Rzip
超分子 | 名称: 1:2 complex of MFRV-VILP bound to IGF1Rzip / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#2 |
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-超分子 #2: MFRV-VILP
超分子 | 名称: MFRV-VILP / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #2 |
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由来(天然) | 生物種: Mandarin fish ranavirus (ウイルス) / Synthetically produced: Yes |
-超分子 #3: IGF1Rzip
超分子 | 名称: IGF1Rzip / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #1 詳細: IGF1R ectodomain with C-terminal leucine zipper domain |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-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: 108.937242 KDa |
組換発現 | 生物種: Cricetulus griseus (モンゴルキヌゲネズミ) |
配列 | 文字列: EICGPGIDIR NDYQQLKRLE NCTVIEGYLH ILLISKAEDY RSYRFPKLTV ITEYLLLFRV AGLESLGDLF PNLTVIRGWK LFYNYALVI FEMTNLKDIG LYNLRNITRG AIRIEKNADL CYLSTVDWSL ILDAVSNNYI VGNKPPKECG DLCPGTMEEK P MCEKTTIN ...文字列: EICGPGIDIR NDYQQLKRLE NCTVIEGYLH ILLISKAEDY RSYRFPKLTV ITEYLLLFRV AGLESLGDLF PNLTVIRGWK LFYNYALVI FEMTNLKDIG LYNLRNITRG AIRIEKNADL CYLSTVDWSL ILDAVSNNYI VGNKPPKECG DLCPGTMEEK P MCEKTTIN NEYNYRCWTT NRCQKMCPST CGKRACTENN ECCHPECLGS CSAPDNDTAC VACRHYYYAG VCVPACPPNT YR FEGWRCV DRDFCANILS AESSDSEGFV IHDGECMQEC PSGFIRNGSQ SMYCIPCEGP CPKVCEEEKK TKTIDSVTSA QML QGCTIF KGNLLINIRR GNNIASELEN FMGLIEVVTG YVKIRHSHAL VSLSFLKNLR LILGEEQLEG NYSFYVLDNQ NLQQ LWDWD HRNLTIKAGK MYFAFNPKLC VSEIYRMEEV TGTKGRQSKG DINTRNNGER ASCESDVLHF TSTTTSKNRI IITWH RYRP PDYRDLISFT VYYKEAPFKN VTEYDGQDAC GSNSWNMVDV DLPPNKDVEP GILLHGLKPW TQYAVYVKAV TLTMVE NDH IRGAKSEILY IRTNASVPSI PLDVLSASNS SSQLIVKWNP PSLPNGNLSY YIVRWQRQPQ DGYLYRHNYC SKDKIPI RK YADGTIDIEE VTENPKTEVC GGEKGPCCAC PKTEAEKQAE KEEAEYRKVF ENFLHNSIFV PRPERKRRDV MQVANTTM S SRSRNTTAAD TYNITDPEEL ETEYPFFESR VDNKERTVIS NLRPFTLYRI DIHSCNHEAE KLGCSASNFV FARTMPAEG ADDIPGPVTW EPRPENSIFL KWPEPENPNG LILMYEIKYG SQVEDQRECV SRQEYRKYGG AKLNRLNPGN YTARIQATSL SGNGSWTDP VFFYVQAKTG YENFIHRMKQ LEDKVEELLS KNYHLENEVA RLKKLVGERS SSEQKLISEE DLN UniProtKB: Insulin-like growth factor 1 receptor |
-分子 #2: Insulin-like growth factor
分子 | 名称: Insulin-like growth factor / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mandarin fish ranavirus (ウイルス) |
分子量 | 理論値: 6.799011 KDa |
配列 | 文字列: VLTDKLCGKD LVDALLLVCG EKGVYSPKMG YARAKTVKGN GIADVCCTSA NGCDLNFLEK FCKT UniProtKB: Insulin-like growth factor |
-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: 11 / 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 | 1.2 mg/mL |
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緩衝液 | pH: 8 |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 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: GLOW DISCHARGE / 前処理 - 時間: 30 sec. / 前処理 - 雰囲気: AIR / 前処理 - 気圧: 0.00039000000000000005 kPa |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
-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 K3 (6k x 4k) / 撮影したグリッド数: 1 / 実像数: 7833 / 平均露光時間: 5.36 sec. / 平均電子線量: 60.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 17.0 µm / 最小 デフォーカス(公称値): 4.0 µm / 倍率(公称値): 130000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |