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- EMDB-20572: Cryo-EM structure of extracellular dimeric complex of RET/GFRAL/GDF15 -
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基本情報
登録情報 | データベース: EMDB / ID: EMD-20572 | |||||||||
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タイトル | Cryo-EM structure of extracellular dimeric complex of RET/GFRAL/GDF15 | |||||||||
![]() | Cryo-EM map of the extracellular complex of RET/GFRAL/GDF15. C2 symmetry was applied in the 3D refinement. | |||||||||
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機能・相同性 | ![]() negative regulation of growth hormone receptor signaling pathway / GDF15-GFRAL signaling pathway / response to metformin / glial cell-derived neurotrophic factor receptor activity / reduction of food intake in response to dietary excess / Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / posterior midgut development / ureter maturation / embryonic epithelial tube formation ...negative regulation of growth hormone receptor signaling pathway / GDF15-GFRAL signaling pathway / response to metformin / glial cell-derived neurotrophic factor receptor activity / reduction of food intake in response to dietary excess / Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / posterior midgut development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / membrane protein proteolysis / positive regulation of peptidyl-serine phosphorylation of STAT protein / Formation of the ureteric bud / positive regulation of neuron maturation / negative regulation of leukocyte migration / Formation of the nephric duct / enteric nervous system development / neuron cell-cell adhesion / positive regulation of fatty acid oxidation / negative regulation of appetite / cellular response to chemical stress / innervation / plasma membrane protein complex / neuron maturation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / stress-activated protein kinase signaling cascade / positive regulation of cell adhesion mediated by integrin / neural crest cell migration / ureteric bud development / negative regulation of multicellular organism growth / positive regulation of myoblast fusion / regulation of axonogenesis / response to pain / negative regulation of SMAD protein signal transduction / homophilic cell adhesion via plasma membrane adhesion molecules / positive regulation of cell size / RET signaling / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of cell adhesion / cellular response to retinoic acid / NPAS4 regulates expression of target genes / transmembrane receptor protein tyrosine kinase activity / transforming growth factor beta receptor signaling pathway / cytokine activity / axon guidance / negative regulation of transforming growth factor beta receptor signaling pathway / growth factor activity / hormone activity / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / positive regulation of neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process / MAPK cascade / actin cytoskeleton / cell-cell signaling / retina development in camera-type eye / signaling receptor activity / nervous system development / RAF/MAP kinase cascade / protein tyrosine kinase activity / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / receptor complex / endosome membrane / positive regulation of cell migration / response to xenobiotic stimulus / external side of plasma membrane / axon / protein phosphorylation / focal adhesion / neuronal cell body / dendrite / calcium ion binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / Golgi apparatus / signal transduction / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.1 Å | |||||||||
![]() | Li J / Shang GJ / Chen YJ / Brautigam CA / Liou J / Zhang XW / Bai XC | |||||||||
![]() | ![]() タイトル: Cryo-EM analyses reveal the common mechanism and diversification in the activation of RET by different ligands. 著者: Jie Li / Guijun Shang / Yu-Ju Chen / Chad A Brautigam / Jen Liou / Xuewu Zhang / Xiao-Chen Bai / ![]() 要旨: RET is a receptor tyrosine kinase (RTK) that plays essential roles in development and has been implicated in several human diseases. Different from most of RTKs, RET requires not only its cognate ...RET is a receptor tyrosine kinase (RTK) that plays essential roles in development and has been implicated in several human diseases. Different from most of RTKs, RET requires not only its cognate ligands but also co-receptors for activation, the mechanisms of which remain unclear due to lack of high-resolution structures of the ligand/co-receptor/receptor complexes. Here, we report cryo-EM structures of the extracellular region ternary complexes of GDF15/GFRAL/RET, GDNF/GFRα1/RET, NRTN/GFRα2/RET and ARTN/GFRα3/RET. These structures reveal that all the four ligand/co-receptor pairs, while using different atomic interactions, induce a specific dimerization mode of RET that is poised to bring the two kinase domains into close proximity for cross-phosphorylation. The NRTN/GFRα2/RET dimeric complex further pack into a tetrameric assembly, which is shown by our cell-based assays to regulate the endocytosis of RET. Our analyses therefore reveal both the common mechanism and diversification in the activation of RET by different ligands. | |||||||||
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「今月の分子」の関連する項目 |
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注釈 | Cryo-EM map of the extracellular complex of RET/GFRAL/GDF15. C2 symmetry was applied in the 3D refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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試料の構成要素
-全体 : RET, GFRAL and GDF15 extracellular complex
全体 | 名称: RET, GFRAL and GDF15 extracellular complex |
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要素 |
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-超分子 #1: RET, GFRAL and GDF15 extracellular complex
超分子 | 名称: RET, GFRAL and GDF15 extracellular complex / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#3 |
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由来(天然) | 生物種: ![]() |
組換発現 | 生物種: ![]() |
分子量 | 理論値: 200 kDa/nm |
-分子 #1: Growth/differentiation factor 15
分子 | 名称: Growth/differentiation factor 15 / タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 14.879113 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MGSSHHHHHH SSGLEVLFQG PHMARNGDHC PLGPGRCCRL HTVRASLEDL GWADWVLSPR EVQVTMCIGA CPSQFRAANM HAQIKTSLH RLKPDTVPAP CCVPASYNPM VLIQKTDTGV SLQTYDDLLA KDCHCI |
-分子 #2: GDNF family receptor alpha-like
分子 | 名称: GDNF family receptor alpha-like / 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: ![]() |
分子量 | 理論値: 39.120598 KDa |
組換発現 | 生物種: ![]() |
配列 | 文字列: QTNNCTYLRE QCLRDANGCK HAWRVMEDAC NDSDPGDPCK MRNSSYCNLS IQYLVESNFQ FKECLCTDDF YCTVNKLLGK KCINKSDNV KEDKFKWNLT TRSHHGFKGM WSCLEVAEAC VGDVVCNAQL ASYLKACSAN GNPCDLKQCQ AAIRFFYQNI P FNIAQMLA ...文字列: QTNNCTYLRE QCLRDANGCK HAWRVMEDAC NDSDPGDPCK MRNSSYCNLS IQYLVESNFQ FKECLCTDDF YCTVNKLLGK KCINKSDNV KEDKFKWNLT TRSHHGFKGM WSCLEVAEAC VGDVVCNAQL ASYLKACSAN GNPCDLKQCQ AAIRFFYQNI P FNIAQMLA FCDCAQSDIP CQQSKEALHS KTCAVNMVPP PTCLSVIRSC QNDELCRRHY RTFQSKCWQR VTRKCHEDEN CI STLSKQD LTCSGSDDCK AAYIDILGTV LQVQCTCRTI TQSEESLCKI FQHMLHRKSC FNYPTLSNVK GMALYTRKHA NKI TLTGFH SPFNGEVGTH HHHHHHH |
-分子 #3: Proto-oncogene tyrosine-protein kinase receptor Ret
分子 | 名称: Proto-oncogene tyrosine-protein kinase receptor Ret / タイプ: protein_or_peptide / ID: 3 / 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: ![]() |
分子量 | 理論値: 69.100812 KDa |
組換発現 | 生物種: ![]() |
配列 | 文字列: LYFSRDAYWE KLYVDQAAGT PLLYVHALRD APEEVPSFRL GQHLYGTYRT RLHENNWICI QEDTGLLYLN RSLDHSSWEK LSVRNHGFP LLTVYLKVFL SPTSLREGEC QWPGCARVYF SFFNTSFPAC SSLKPRELCF PETRPSFRIR ENRPPGTFHQ F RLLPVQFL ...文字列: LYFSRDAYWE KLYVDQAAGT PLLYVHALRD APEEVPSFRL GQHLYGTYRT RLHENNWICI QEDTGLLYLN RSLDHSSWEK LSVRNHGFP LLTVYLKVFL SPTSLREGEC QWPGCARVYF SFFNTSFPAC SSLKPRELCF PETRPSFRIR ENRPPGTFHQ F RLLPVQFL CPNISVAYRL LEGEGLPFRC APDSLEVSTR WALDREQREK YELVAVCTVH AGAREEVVMV PFPVTVYDED DS APTFPAG VDTASAVVEF KRKEDTVVAT LRVFDADVVP ASGELVRRYT STLLPGDTWA QQTFRVEHWP NETSVQANGS FVR ATVHDY RLVLNRNLSI SENRTMQLAV LVNDSDFQGP GAGVLLLHFN VSVLPVSLHL PSTYSLSVSR RARRFAQIGK VCVE NCQAF SGINVQYKLH SSGANCSTLG VVTSAEDTSG ILFVNDTKAL RRPKCAELHY MVVATDQQTS RQAQAQLLVT VEGSY VAEE AGCPLSCAVS KRRLECEECG GLGSPTGRCE WRQGDGKGIT RNFSTCSPST KTCPDGHCDV VETQDINICP QDCLRG SIV GGHEPGEPRG IKAGYGTCNC FPEEEKCFCE PEDIQDPLCD ELCRGTHHHH HHHH |
-分子 #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
分子 | 名称: 2-acetamido-2-deoxy-beta-D-glucopyranose / タイプ: ligand / ID: 4 / コピー数: 14 / 式: NAG |
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分子量 | 理論値: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-分子 #5: CALCIUM ION
分子 | 名称: CALCIUM ION / タイプ: ligand / ID: 5 / コピー数: 8 / 式: CA |
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分子量 | 理論値: 40.078 Da |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 1 mg/mL |
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緩衝液 | pH: 7.4 |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE |
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 |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | 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 |
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 / デジタル化 - 画像ごとのフレーム数: 1-30 / 撮影したグリッド数: 1 / 平均露光時間: 15.0 sec. / 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 70.0 µm / 倍率(補正後): 46729 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm |
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 |
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画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT / 温度因子: 190 |
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得られたモデル | ![]() PDB-6q2j: |