+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6um2 | ||||||
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タイトル | Structure of M-6-P/IGFII Receptor and IGFII complex | ||||||
要素 |
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キーワード | SUGAR BINDING PROTEIN / M-6-P / IGFII / receptor | ||||||
機能・相同性 | 機能・相同性情報 kringle domain binding / spongiotrophoblast cell proliferation / negative regulation of muscle cell differentiation / positive regulation of skeletal muscle tissue growth / embryonic placenta morphogenesis / regulation of muscle cell differentiation / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / genomic imprinting ...kringle domain binding / spongiotrophoblast cell proliferation / negative regulation of muscle cell differentiation / positive regulation of skeletal muscle tissue growth / embryonic placenta morphogenesis / regulation of muscle cell differentiation / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / genomic imprinting / positive regulation of organ growth / exocrine pancreas development / positive regulation of multicellular organism growth / lysosomal transport / positive regulation of vascular endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of activated T cell proliferation / D-mannose binding / endocytic vesicle / positive regulation of cell division / positive regulation of glycogen biosynthetic process / embryonic placenta development / SHC-related events triggered by IGF1R / positive regulation of insulin receptor signaling pathway / insulin-like growth factor receptor binding / striated muscle cell differentiation / positive regulation of mitotic nuclear division / protein serine/threonine kinase activator activity / insulin-like growth factor receptor signaling pathway / platelet alpha granule lumen / animal organ morphogenesis / phosphoprotein binding / insulin receptor binding / growth factor activity / trans-Golgi network / hormone activity / osteoblast differentiation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / glucose metabolic process / integrin binding / late endosome / Platelet degranulation / insulin receptor signaling pathway / signaling receptor activity / in utero embryonic development / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome membrane / receptor ligand activity / Golgi membrane / positive regulation of cell population proliferation / regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Bos taurus (ウシ) | ||||||
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: 4.32 Å | ||||||
データ登録者 | Wang, R. / Qi, X. / Li, X. | ||||||
引用 | ジャーナル: Sci Adv / 年: 2020 タイトル: Marked structural rearrangement of mannose 6-phosphate/IGF2 receptor at different pH environments. 著者: Rong Wang / Xiaofeng Qi / Philip Schmiege / Elias Coutavas / Xiaochun Li / 要旨: Many cell surface receptors internalize their ligands and deliver them to endosomes, where the acidic pH causes the ligand to dissociate. The liberated receptor returns to the cell surface in a ...Many cell surface receptors internalize their ligands and deliver them to endosomes, where the acidic pH causes the ligand to dissociate. The liberated receptor returns to the cell surface in a process called receptor cycling. The structural basis for pH-dependent ligand dissociation is not well understood. In some receptors, the ligand binding domain is composed of multiple repeated sequences. The insulin-like growth factor 2 receptor (IGF2R) contains 15 β strand-rich repeat domains. The overall structure and the mechanism by which IGF2R binds IGF2 and releases it are unknown. We used cryo-EM to determine the structures of the IGF2R at pH 7.4 with IGF2 bound and at pH 4.5 in the ligand-dissociated state. The results reveal different arrangements of the receptor in different pH environments mediated by changes in the interactions between the repeated sequences. These results have implications for our understanding of ligand release from receptors in endocytic compartments. | ||||||
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 | 6um2.cif.gz | 326.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6um2.ent.gz | 249.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6um2.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 | 6um2_validation.pdf.gz | 789.6 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6um2_full_validation.pdf.gz | 812.9 KB | 表示 | |
XML形式データ | 6um2_validation.xml.gz | 50.1 KB | 表示 | |
CIF形式データ | 6um2_validation.cif.gz | 75.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/um/6um2 ftp://data.pdbj.org/pub/pdb/validation_reports/um/6um2 | 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: 274830.125 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P08169 | ||
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#2: タンパク質 | 分子量: 7615.667 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: IGF2, PP1446 / 発現宿主: Escherichia coli K-12 (大腸菌) / 参照: UniProt: P01344 | ||
#3: 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 |
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由来(天然) |
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由来(組換発現) | 生物種: Escherichia coli K-12 (大腸菌) | ||||||||||||||||||||||||
緩衝液 | pH: 7.4 | ||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE |
-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: DARK FIELD |
撮影 | 電子線照射量: 100 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
ソフトウェア | 名称: REFMAC / バージョン: 5.8.0238 / 分類: 精密化 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF補正 | タイプ: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.32 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 75821 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | 解像度: 4.32→302.72 Å / Cor.coef. Fo:Fc: 0.76 / SU B: 65.401 / SU ML: 0.813 / ESU R: 0.29 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 19.059 Å2
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精密化ステップ | サイクル: 1 / 合計: 13094 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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