+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-22098 | |||||||||
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タイトル | Interleukin-10 signaling complex with IL-10RA and IL-10RB | |||||||||
マップデータ | Sharpened map of the hexameric Interleukin-10 signaling complex with IL-10RA and IL-10RB | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 interleukin-10 binding / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor activity / interleukin-10 receptor binding / regulation of response to wounding / interleukin-28 receptor complex / negative regulation of cytokine activity / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation / negative regulation of interferon-alpha production ...interleukin-10 binding / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor activity / interleukin-10 receptor binding / regulation of response to wounding / interleukin-28 receptor complex / negative regulation of cytokine activity / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation / negative regulation of interferon-alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / response to carbon monoxide / positive regulation of plasma cell differentiation / positive regulation of B cell apoptotic process / ubiquitin-dependent endocytosis / response to inactivity / chronic inflammatory response to antigenic stimulus / cytoplasmic sequestering of NF-kappaB / intestinal epithelial structure maintenance / negative regulation of membrane protein ectodomain proteolysis / regulation of isotype switching / positive regulation of cellular respiration / negative regulation of heterotypic cell-cell adhesion / negative regulation of cytokine production involved in immune response / type III interferon-mediated signaling pathway / negative regulation of interleukin-1 production / negative regulation of MHC class II biosynthetic process / branching involved in labyrinthine layer morphogenesis / negative regulation of interleukin-8 production / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / type 2 immune response / endothelial cell apoptotic process / positive regulation of macrophage activation / positive regulation of MHC class II biosynthetic process / leukocyte chemotaxis / positive regulation of signaling receptor activity / positive regulation of heterotypic cell-cell adhesion / negative regulation of cytokine production / CD163 mediating an anti-inflammatory response / cellular response to hepatocyte growth factor stimulus / Other interleukin signaling / Interleukin-20 family signaling / regulation of synapse organization / positive regulation of sprouting angiogenesis / B cell proliferation / negative regulation of B cell proliferation / defense response to protozoan / negative regulation of vascular associated smooth muscle cell proliferation / Interleukin-10 signaling / negative regulation of interleukin-6 production / 造血 / negative regulation of type II interferon production / positive regulation of immunoglobulin production / negative regulation of tumor necrosis factor production / negative regulation of mitotic cell cycle / positive regulation of cell cycle / response to glucocorticoid / negative regulation of T cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of endothelial cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of autophagy / B cell differentiation / FCGR3A-mediated IL10 synthesis / response to activity / cellular response to estradiol stimulus / cytokine activity / liver regeneration / positive regulation of cytokine production / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / response to insulin / response to molecule of bacterial origin / cellular response to virus / negative regulation of inflammatory response / positive regulation of miRNA transcription / positive regulation of DNA-binding transcription factor activity / cytokine-mediated signaling pathway / signaling receptor activity / 遺伝子発現の調節 / Interleukin-4 and Interleukin-13 signaling / defense response to virus / cellular response to lipopolysaccharide / response to lipopolysaccharide / protein dimerization activity / defense response to bacterium / 免疫応答 / response to xenobiotic stimulus / 炎症 / apical plasma membrane / negative regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / シグナル伝達 / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / 生体膜 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.5 Å | |||||||||
データ登録者 | Saxton RA / Tsutsumi N / Gati C / Garcia KC | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Science / 年: 2021 タイトル: Structure-based decoupling of the pro- and anti-inflammatory functions of interleukin-10. 著者: Robert A Saxton / Naotaka Tsutsumi / Leon L Su / Gita C Abhiraman / Kritika Mohan / Lukas T Henneberg / Nanda G Aduri / Cornelius Gati / K Christopher Garcia / 要旨: Interleukin-10 (IL-10) is an immunoregulatory cytokine with both anti-inflammatory and immunostimulatory properties and is frequently dysregulated in disease. We used a structure-based approach to ...Interleukin-10 (IL-10) is an immunoregulatory cytokine with both anti-inflammatory and immunostimulatory properties and is frequently dysregulated in disease. We used a structure-based approach to deconvolute IL-10 pleiotropy by determining the structure of the IL-10 receptor (IL-10R) complex by cryo-electron microscopy at a resolution of 3.5 angstroms. The hexameric structure shows how IL-10 and IL-10Rα form a composite surface to engage the shared signaling receptor IL-10Rβ, enabling the design of partial agonists. IL-10 variants with a range of IL-10Rβ binding strengths uncovered substantial differences in response thresholds across immune cell populations, providing a means of manipulating IL-10 cell type selectivity. Some variants displayed myeloid-biased activity by suppressing macrophage activation without stimulating inflammatory CD8 T cells, thereby uncoupling the major opposing functions of IL-10. These results provide a mechanistic blueprint for tuning the pleiotropic actions of IL-10. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_22098.map.gz | 59.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-22098-v30.xml emd-22098.xml | 19.7 KB 19.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_22098.png | 269.4 KB | ||
その他 | emd_22098_additional_1.map.gz | 32.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-22098 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22098 | HTTPS FTP |
-関連構造データ
関連構造データ | 6x93MC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10557 (タイトル: Interleukin-10 signaling complex with IL-10RA and IL-10RB Data size: 5.4 TB Data #1: Unaligned dark-subtracted TIFF movies with a gain reference for the 3D reconstruction of EMD-22098. [micrographs - multiframe]) |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_22098.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Sharpened map of the hexameric Interleukin-10 signaling complex with IL-10RA and IL-10RB | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.078 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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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
-追加マップ: Unsharpened map of the hexameric Interleukin-10 signaling complex...
ファイル | emd_22098_additional_1.map | ||||||||||||
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注釈 | Unsharpened map of the hexameric Interleukin-10 signaling complex with IL-10RA and IL-10RB | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Interleukin-10 signaling complex with IL-10RA and IL-10RB
全体 | 名称: Interleukin-10 signaling complex with IL-10RA and IL-10RB |
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要素 |
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-超分子 #1: Interleukin-10 signaling complex with IL-10RA and IL-10RB
超分子 | 名称: Interleukin-10 signaling complex with IL-10RA and IL-10RB タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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分子量 | 理論値: 130 KDa |
-超分子 #2: Interleukin-10, IL-10RA
超分子 | 名称: Interleukin-10, IL-10RA / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1-#2 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) |
-超分子 #3: IL-10RB
超分子 | 名称: IL-10RB / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #3 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
-分子 #1: Interleukin-10
分子 | 名称: Interleukin-10 / 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: Homo sapiens (ヒト) |
分子量 | 理論値: 18.778543 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: SPGQGTQSEN SCTHFPGYLP NMLRDLRDAF SRVKTFFQMK DQLDNLLLKE SLLEDFKGYL GCQALSEMIQ FYLEEVMPQA ENQDPDIKA HVQSLGENLK DLRLWLRRCH RFLPCENKSK AVEQVKNAFN KLQEKGIYKA MSEFDIFINY IEAYMTMKIR N |
-分子 #2: Interleukin-10 receptor subunit alpha
分子 | 名称: Interleukin-10 receptor subunit alpha / 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: Homo sapiens (ヒト) |
分子量 | 理論値: 24.422391 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: HGTELPSPPS VWFEAEFFHH ILHWTPIPNQ SESTCYEVAL LRYGIESWNS ISNCSQTLSY DLTAVTLDLY HSNGYRARVR AVDGSRHSN WTVTNTRFSV DEVTLTVGSV NLEIHNGFIL GKIQLPRPKM APANDTYESI FSHFREYEIA IRKVPGNFTF T HKKVKHEN ...文字列: HGTELPSPPS VWFEAEFFHH ILHWTPIPNQ SESTCYEVAL LRYGIESWNS ISNCSQTLSY DLTAVTLDLY HSNGYRARVR AVDGSRHSN WTVTNTRFSV DEVTLTVGSV NLEIHNGFIL GKIQLPRPKM APANDTYESI FSHFREYEIA IRKVPGNFTF T HKKVKHEN FSLLTSGEVG EFCVQVKPSV ASRSNKGMWS KEECISLTRQ YFTVTN |
-分子 #3: Interleukin-10 receptor subunit beta
分子 | 名称: Interleukin-10 receptor subunit beta / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 23.569334 KDa |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
配列 | 文字列: MVPPPENVRM NSVNFKNILQ WESPAFAKGQ LTFTAQYLSY RIFQDKCMQT TLTECDFSSL SKYGDHTLRV RAEFADEHSD WVQITFCPV DDTIIGPPGM QVEVLADSLH MRFLAPKIEN EYETWTMKNV YNSWTYNVQY WKNGTDEKFQ ITPQYDFEVL R NLEPWTTY ...文字列: MVPPPENVRM NSVNFKNILQ WESPAFAKGQ LTFTAQYLSY RIFQDKCMQT TLTECDFSSL SKYGDHTLRV RAEFADEHSD WVQITFCPV DDTIIGPPGM QVEVLADSLH MRFLAPKIEN EYETWTMKNV YNSWTYNVQY WKNGTDEKFQ ITPQYDFEVL R NLEPWTTY CVQVRGFLPD RNKAGEWSEP VCEQTTHDET VPS |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 10 mg/mL | ||||||||||||
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緩衝液 | pH: 7.2 構成要素:
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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: 95 % / チャンバー内温度: 293 K / 装置: LEICA EM GP / 詳細: 5s blotting. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 100.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 最大 デフォーカス(公称値): -2.0 µm / 最小 デフォーカス(公称値): -0.8 µm / 倍率(公称値): 81000 |
特殊光学系 | エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 20 eV |
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 |
撮影 | 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: 9413 / 平均電子線量: 50.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
粒子像選択 | 選択した数: 6701298 |
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CTF補正 | ソフトウェア - 名称: cryoSPARC |
初期モデル | モデルのタイプ: OTHER / 詳細: Initial model generation in cryoSPARC. |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: cryoSPARC |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: cryoSPARC |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: cryoSPARC / 使用した粒子像数: 86725 |