+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6q2s | ||||||
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タイトル | Cryo-EM structure of RET/GFRa3/ARTN extracellular complex. The 3D refinement was applied with C2 symmetry. | ||||||
要素 |
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キーワード | SIGNALING PROTEIN / RET / receptor tyrosine kinase / cryo-EM | ||||||
機能・相同性 | 機能・相同性情報 glial cell-derived neurotrophic factor receptor activity / glial cell-derived neurotrophic factor receptor binding / GDF15-GFRAL signaling pathway / 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 ...glial cell-derived neurotrophic factor receptor activity / glial cell-derived neurotrophic factor receptor binding / GDF15-GFRAL signaling pathway / 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 / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / membrane protein proteolysis / positive regulation of peptidyl-serine phosphorylation of STAT protein / axon guidance receptor activity / Formation of the ureteric bud / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / positive regulation of neuron maturation / neuron cell-cell adhesion / septin ring / Formation of the nephric duct / enteric nervous system development / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / sympathetic nervous system development / peripheral nervous system development / innervation / induction of positive chemotaxis / SUMOylation of SUMOylation proteins / plasma membrane protein complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / neuron maturation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / SUMOylation of RNA binding proteins / NCAM1 interactions / positive regulation of cell adhesion mediated by integrin / SUMOylation of chromatin organization proteins / neural crest cell migration / ureteric bud development / regulation of axonogenesis / extrinsic component of membrane / response to pain / homophilic cell adhesion via plasma membrane adhesion molecules / ubiquitin-like protein ligase binding / protein sumoylation / positive regulation of cell size / RET signaling / condensed nuclear chromosome / neuroblast proliferation / transmembrane receptor protein tyrosine kinase activity / regulation of cell adhesion / cellular response to retinoic acid / NPAS4 regulates expression of target genes / axon guidance / receptor protein-tyrosine kinase / growth factor activity / neuron migration / receptor tyrosine kinase binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron projection development / protein tag activity / MAPK cascade / retina development in camera-type eye / signaling receptor activity / nervous system development / RAF/MAP kinase cascade / protein tyrosine kinase activity / receptor complex / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome membrane / early endosome / positive regulation of cell migration / response to xenobiotic stimulus / protein phosphorylation / external side of plasma membrane / axon / signaling receptor binding / neuronal cell body / dendrite / calcium ion binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / signal transduction / extracellular space / extracellular region / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Saccharomyces cerevisiae (パン酵母) Homo sapiens (ヒト) | ||||||
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: 3.8 Å | ||||||
データ登録者 | Li, J. / Shang, G.J. / Chen, Y.J. / Brautigam, C.A. / Liou, J. / Zhang, X.W. / Bai, X.C. | ||||||
引用 | ジャーナル: Elife / 年: 2019 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. | ||||||
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 | 6q2s.cif.gz | 326.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6q2s.ent.gz | 258.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6q2s.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 | 6q2s_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6q2s_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | 6q2s_validation.xml.gz | 50.7 KB | 表示 | |
CIF形式データ | 6q2s_validation.cif.gz | 75.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/q2/6q2s ftp://data.pdbj.org/pub/pdb/validation_reports/q2/6q2s | 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 | 分子量: 25793.287 Da / 分子数: 2 / 由来タイプ: 組換発現 詳細: A SUMO protein was fused to the N-terminal of NRTN for the protein expression 由来: (組換発現) Saccharomyces cerevisiae (パン酵母), (組換発現) Homo sapiens (ヒト) 遺伝子: SMT3, ARTN, EVN / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q12306, UniProt: Q5T4W7 #2: タンパク質 | 分子量: 38370.023 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GFRA3, UNQ339/PRO538/PRO3664 / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O60609 #3: タンパク質 | 分子量: 69100.812 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RET, CDHF12, CDHR16, PTC, RET51 / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P07949, receptor protein-tyrosine kinase #4: 糖 | ChemComp-NAG / #5: 化合物 | ChemComp-CA / 研究の焦点であるリガンドがあるか | Y | |
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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 |
-試料調製
構成要素 | 名称: RET, GFRAL and GDF15 extracellular complex / タイプ: COMPLEX / Entity ID: #1-#3 / 由来: RECOMBINANT |
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分子量 | 値: 200 kDa/nm / 実験値: NO |
由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 7.4 |
試料 | 濃度: 1 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: unspecified |
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 |
-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(補正後): 46729 X / Cs: 2.7 mm / C2レンズ絞り径: 70 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: 15 sec. / 電子線照射量: 50 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) 撮影したグリッド数: 1 |
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: 30 / 利用したフレーム数/画像: 1-30 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
対称性 | 点対称性: C2 (2回回転対称) | ||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 114344 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||
原子モデル構築 | B value: 190 / プロトコル: FLEXIBLE FIT / 空間: REAL |