+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7wrq | ||||||
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タイトル | Structure of Human IGF1/IGFBP3/ALS Ternary Complex | ||||||
要素 |
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キーワード | SIGNALING PROTEIN / Growth / Proliferation / Differentiation / Metabolism | ||||||
機能・相同性 | 機能・相同性情報 protein tyrosine phosphatase activator activity / regulation of insulin-like growth factor receptor signaling pathway / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / proteoglycan biosynthetic process / negative regulation of smooth muscle cell migration ...protein tyrosine phosphatase activator activity / regulation of insulin-like growth factor receptor signaling pathway / glycolate metabolic process / muscle hypertrophy / negative regulation of oocyte development / positive regulation of trophectodermal cell proliferation / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / proteoglycan biosynthetic process / negative regulation of smooth muscle cell migration / positive regulation of glycoprotein biosynthetic process / myotube cell development / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / negative regulation of neuroinflammatory response / bone mineralization involved in bone maturation / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / positive regulation of cell growth involved in cardiac muscle cell development / negative regulation of vascular associated smooth muscle cell apoptotic process / IRS-related events triggered by IGF1R / insulin-like growth factor binding / exocytic vesicle / cell activation / positive regulation of calcineurin-NFAT signaling cascade / insulin-like growth factor II binding / type B pancreatic cell proliferation / positive regulation of transcription regulatory region DNA binding / insulin-like growth factor I binding / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of Ras protein signal transduction / myoblast differentiation / positive regulation of insulin-like growth factor receptor signaling pathway / myoblast proliferation / muscle organ development / negative regulation of interleukin-1 beta production / TP53 Regulates Transcription of Death Receptors and Ligands / positive regulation of cardiac muscle hypertrophy / positive regulation of smooth muscle cell migration / positive regulation of activated T cell proliferation / negative regulation of release of cytochrome c from mitochondria / negative regulation of amyloid-beta formation / negative regulation of smooth muscle cell apoptotic process / fibronectin binding / negative regulation of tumor necrosis factor production / regulation of glucose metabolic process / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / epithelial to mesenchymal transition / positive regulation of myoblast differentiation / SHC-related events triggered by IGF1R / positive regulation of DNA binding / positive regulation of osteoblast differentiation / negative regulation of signal transduction / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of glycolytic process / activation of protein kinase B activity / positive regulation of mitotic nuclear division / extracellular matrix / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / negative regulation of protein phosphorylation / skeletal system development / positive regulation of epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein secretion / positive regulation of glucose import / regulation of cell growth / Post-translational protein phosphorylation / positive regulation of smooth muscle cell proliferation / negative regulation of smooth muscle cell proliferation / regulation of protein phosphorylation / insulin-like growth factor receptor binding / growth factor activity / wound healing / insulin receptor binding / hormone activity / osteoblast differentiation / cellular response to amyloid-beta / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of peptidyl-tyrosine phosphorylation / MAPK cascade / positive regulation of fibroblast proliferation / integrin binding / Platelet degranulation / response to heat / regulation of gene expression / cell population proliferation / Ras protein signal transduction / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / protein stabilization / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / endoplasmic reticulum lumen / protein phosphorylation / negative regulation of gene expression / apoptotic process 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: 3.6 Å | ||||||
データ登録者 | Kim, H. / Fu, Y. / Kim, H.M. | ||||||
資金援助 | 1件
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引用 | ジャーナル: Nat Commun / 年: 2022 タイトル: Structural basis for assembly and disassembly of the IGF/IGFBP/ALS ternary complex 著者: Kim, H. / Fu, Y. / Hong, H.J. / Lee, S.G. / Lee, D.S. / Kim, H.M. | ||||||
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 | 7wrq.cif.gz | 149.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7wrq.ent.gz | 118 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7wrq.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 | 7wrq_validation.pdf.gz | 1.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7wrq_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 7wrq_validation.xml.gz | 39.7 KB | 表示 | |
CIF形式データ | 7wrq_validation.cif.gz | 57.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/wr/7wrq ftp://data.pdbj.org/pub/pdb/validation_reports/wr/7wrq | HTTPS FTP |
-関連構造データ
関連構造データ | 32735MC 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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1 |
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-要素
#1: タンパク質 | 分子量: 63312.316 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ALS / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P35858 | ||
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#2: タンパク質 | 分子量: 28794.740 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IGFBP3 / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P17936 | ||
#3: タンパク質 | 分子量: 7663.752 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: IGF1 / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P05019 | ||
#4: 多糖 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||
#5: 糖 | ChemComp-NAG / 研究の焦点であるリガンドがあるか | N | |
-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: Ternary complex of IGF1/IGFBP3/ALS / タイプ: COMPLEX / Entity ID: #1-#3 / 由来: RECOMBINANT | |||||||||||||||
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分子量 | 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: 8 | |||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.4 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: 15mA / グリッドの材料: COPPER / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 | |||||||||||||||
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: 277.15 K / 詳細: blot for 2 seconds before plunging |
-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: CDS mode is used |
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(公称値): 105000 X / 最大 デフォーカス(公称値): 2700 nm / 最小 デフォーカス(公称値): 900 nm / Cs: 2.7 mm |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 平均露光時間: 3.4 sec. / 電子線照射量: 63.23033928 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 / 実像数: 14754 |
-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: C1 (非対称) | ||||||||||||
3次元再構成 | 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 638058 / クラス平均像の数: 1 / 対称性のタイプ: POINT |