+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8dfp | ||||||
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タイトル | Ectodomain of full-length KIT(DupA502,Y503)-SCF dimers | ||||||
要素 |
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キーワード | TRANSFERASE (転移酵素) / receptor tyrosine kinase (受容体型チロシンキナーゼ) / cell signaling / cancer (悪性腫瘍) / cryo-EM (低温電子顕微鏡法) / KIT / stem cell factor / oncogenic mutant / extracellular domain / asymmetric interface / structural plasticity | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of myeloid leukocyte differentiation / negative regulation of mast cell apoptotic process / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of hematopoietic stem cell proliferation / Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants ...positive regulation of myeloid leukocyte differentiation / negative regulation of mast cell apoptotic process / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic progenitor cell differentiation / positive regulation of hematopoietic stem cell proliferation / Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants / Nilotinib-resistant KIT mutants / Regorafenib-resistant KIT mutants / Signaling by kinase domain mutants of KIT / Sunitinib-resistant KIT mutants / Signaling by juxtamembrane domain KIT mutants / Sorafenib-resistant KIT mutants / Signaling by extracellular domain mutants of KIT / stem cell factor receptor activity / hematopoietic stem cell migration / melanocyte adhesion / positive regulation of pyloric antrum smooth muscle contraction / positive regulation of colon smooth muscle contraction / erythropoietin-mediated signaling pathway / positive regulation of vascular associated smooth muscle cell differentiation / melanocyte migration / positive regulation of dendritic cell cytokine production / myeloid leukocyte differentiation / Kit signaling pathway / positive regulation of melanocyte differentiation / regulation of bile acid metabolic process / positive regulation of small intestine smooth muscle contraction / mast cell apoptotic process / mast cell differentiation / positive regulation of mast cell proliferation / mast cell chemotaxis / Fc receptor signaling pathway / glycosphingolipid metabolic process / mast cell proliferation / positive regulation of long-term neuronal synaptic plasticity / detection of mechanical stimulus involved in sensory perception of sound / positive regulation of pseudopodium assembly / positive regulation of mast cell cytokine production / immature B cell differentiation / melanocyte differentiation / lymphoid progenitor cell differentiation / germ cell migration / myeloid progenitor cell differentiation / digestive tract development / positive regulation of Ras protein signal transduction / negative regulation of programmed cell death / 神経堤 / embryonic hemopoiesis / positive regulation of leukocyte migration / 顔料 / lamellipodium assembly / tongue development / megakaryocyte development / Regulation of KIT signaling / stem cell population maintenance / mast cell degranulation / positive regulation of Notch signaling pathway / cytokine binding / negative regulation of reproductive process / negative regulation of developmental process / growth factor binding / somatic stem cell population maintenance / 造血 / T cell differentiation / spermatid development / ectopic germ cell programmed cell death / hematopoietic progenitor cell differentiation / : / response to cadmium ion / T cell proliferation / positive regulation of T cell proliferation / ovarian follicle development / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / SH2 domain binding / transmembrane receptor protein tyrosine kinase activity / cell chemotaxis / B cell differentiation / 赤血球形成 / acrosomal vesicle / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / epithelial cell proliferation / filopodium / cytokine activity / 細胞分化 / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / visual learning / Signaling by SCF-KIT / response to organic cyclic compound / 受容体型チロシンキナーゼ / cytoplasmic side of plasma membrane / 核小体 / cytokine-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity 類似検索 - 分子機能 | ||||||
生物種 | 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: 3.17 Å | ||||||
データ登録者 | Bertoletti, N. / Krimmer, S.G. / Mi, W. / Schlessinger, J. | ||||||
資金援助 | 1件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2023 タイトル: Cryo-EM analyses of KIT and oncogenic mutants reveal structural oncogenic plasticity and a target for therapeutic intervention. 著者: Stefan G Krimmer / Nicole Bertoletti / Yoshihisa Suzuki / Luka Katic / Jyotidarsini Mohanty / Sheng Shu / Sangwon Lee / Irit Lax / Wei Mi / Joseph Schlessinger / 要旨: The receptor tyrosine kinase KIT and its ligand stem cell factor (SCF) are required for the development of hematopoietic stem cells, germ cells, and other cells. A variety of human cancers, such as ...The receptor tyrosine kinase KIT and its ligand stem cell factor (SCF) are required for the development of hematopoietic stem cells, germ cells, and other cells. A variety of human cancers, such as acute myeloid leukemia, gastrointestinal stromal tumor, and mast cell leukemia, are driven by somatic gain-of-function KIT mutations. Here, we report cryo electron microscopy (cryo-EM) structural analyses of full-length wild-type and two oncogenic KIT mutants, which show that the overall symmetric arrangement of the extracellular domain of ligand-occupied KIT dimers contains asymmetric D5 homotypic contacts juxtaposing the plasma membrane. Mutational analysis of KIT reveals in D5 region an "Achilles heel" for therapeutic intervention. A ligand-sensitized oncogenic KIT mutant exhibits a more comprehensive and stable D5 asymmetric conformation. A constitutively active ligand-independent oncogenic KIT mutant adopts a V-shaped conformation solely held by D5-mediated contacts. Binding of SCF to this mutant fully restores the conformation of wild-type KIT dimers, including the formation of salt bridges responsible for D4 homotypic contacts and other hallmarks of SCF-induced KIT dimerization. These experiments reveal an unexpected structural plasticity of oncogenic KIT mutants and a therapeutic target in D5. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8dfp.cif.gz | 411.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8dfp.ent.gz | 328.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8dfp.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/df/8dfp ftp://data.pdbj.org/pub/pdb/validation_reports/df/8dfp | HTTPS FTP |
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-関連構造データ
関連構造データ | 27410MC 8dfmC 8dfqC M: このデータのモデリングに利用したマップデータ 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
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 110891.258 Da / 分子数: 2 / 変異: K619A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KIT, SCFR 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P10721, 受容体型チロシンキナーゼ #2: タンパク質 | 分子量: 14742.981 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: KITLG, MGF, SCF / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): CodonPlus RIPL / 参照: UniProt: P21583 #3: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #4: 糖 | 研究の焦点であるリガンドがあるか | N | |
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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: Full-length KIT(DupA502,Y503)-SCF dimers reconstituted in amphipol タイプ: COMPLEX / Entity ID: #1-#2 / 由来: RECOMBINANT | ||||||||||||||||||||
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分子量 | 値: 0.25 MDa / 実験値: YES | ||||||||||||||||||||
由来(天然) | 生物種: Homo sapiens (ヒト) / 細胞内の位置: membrane | ||||||||||||||||||||
由来(組換発現) | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) プラスミド: Bacmid | ||||||||||||||||||||
緩衝液 | pH: 7.4 | ||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 5.6 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: This sample was monodisperse. | ||||||||||||||||||||
試料支持 | グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: C-flat-1.2/1.3 | ||||||||||||||||||||
急速凍結 | 装置: GATAN CRYOPLUNGE 3 / 凍結剤: ETHANE / 湿度: 90 % / 凍結前の試料温度: 293 K / 詳細: Blotting time 3 sec, blotting force 0. |
-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 / 詳細: SerialEM COMA-FREE ALIGNMENT |
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 FIELDBright-field microscopy / 倍率(公称値): 64000 X / 最大 デフォーカス(公称値): 2200 nm / 最小 デフォーカス(公称値): 1200 nm / Cs: 2.7 mm |
試料ホルダ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 11.134 sec. / 電子線照射量: 64.52 e/Å2 / 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: 8456 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / 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: 3649954 | ||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.17 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 865760 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 119.4 / プロトコル: RIGID BODY FIT / 空間: REAL | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 8DFM | ||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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