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基本情報
登録情報 | データベース: PDB / ID: 5ijb | ||||||||||||
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タイトル | The ligand-free structure of the mouse TLR4/MD-2 complex | ||||||||||||
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![]() | IMMUNE SYSTEM / leucine-rich repeats | ||||||||||||
機能・相同性 | ![]() MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / Heme signaling / nitric oxide production involved in inflammatory response / Regulation of TLR by endogenous ligand / TRIF-mediated programmed cell death / MHC class II biosynthetic process / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex ...MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / Heme signaling / nitric oxide production involved in inflammatory response / Regulation of TLR by endogenous ligand / TRIF-mediated programmed cell death / MHC class II biosynthetic process / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / lipopolysaccharide immune receptor activity / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of matrix metallopeptidase secretion / IKK complex recruitment mediated by RIP1 / Toll-like receptor 4 binding / mast cell activation / lipopolysaccharide receptor complex / positive regulation of lymphocyte proliferation / detection of lipopolysaccharide / regulation of dendritic cell cytokine production / lymphocyte proliferation / negative regulation of interleukin-23 production / cellular response to oxidised low-density lipoprotein particle stimulus / wound healing involved in inflammatory response / B cell proliferation involved in immune response / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / activation of NF-kappaB-inducing kinase activity / positive regulation of stress-activated MAPK cascade / intestinal epithelial structure maintenance / positive regulation of interleukin-1 production / positive regulation of interleukin-13 production / macrophage activation / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / microglia differentiation / NAD+ nucleosidase activity, cyclic ADP-ribose generating / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / positive regulation of platelet activation / positive regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of interleukin-17 production / positive regulation of cytokine production involved in inflammatory response / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of cold-induced thermogenesis / positive regulation of macrophage cytokine production / MyD88-dependent toll-like receptor signaling pathway / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / positive regulation of smooth muscle cell migration / positive regulation of reactive oxygen species biosynthetic process / positive regulation of NLRP3 inflammasome complex assembly / cellular response to lipoteichoic acid / negative regulation of interleukin-6 production / positive regulation of interferon-alpha production / negative regulation of type II interferon production / B cell proliferation / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / phagocytic cup / phagocytosis / stress-activated MAPK cascade / positive regulation of chemokine production / JNK cascade / cellular response to platelet-derived growth factor stimulus / neurogenesis / ruffle / positive regulation of B cell proliferation / nitric oxide biosynthetic process / positive regulation of interleukin-12 production / ERK1 and ERK2 cascade / positive regulation of MAP kinase activity / activation of innate immune response / positive regulation of interferon-beta production / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / response to bacterium / positive regulation of smooth muscle cell proliferation / positive regulation of JNK cascade / lipopolysaccharide binding / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of type II interferon production / cellular response to mechanical stimulus / positive regulation of inflammatory response / cellular response to amyloid-beta / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / cellular response to lipopolysaccharide / regulation of inflammatory response 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() ![]() ![]() | ||||||||||||
手法 | ![]() ![]() ![]() | ||||||||||||
![]() | Wang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K. ...Wang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K. / Moresco, E.M. / Berger, M. / Zhan, X. / Zhang, H. / Boger, D.L. / Beutler, B. | ||||||||||||
![]() | ![]() タイトル: TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS. 著者: Wang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M.M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K.W. / Moresco, E.M. / Berger, M. / Zhan, X. / Zhang, H. / Boger, D.L. / Beutler, B. | ||||||||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 596 KB | 表示 | ![]() |
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PDB形式 | ![]() | 497.2 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 2.3 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2.4 MB | 表示 | |
XML形式データ | ![]() | 54.5 KB | 表示 | |
CIF形式データ | ![]() | 73.8 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 67280.703 Da / 分子数: 2 断片: TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200) 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() ![]() 遺伝子: Tlr4, Lps, VLRB 発現宿主: ![]() ![]() 参照: UniProt: Q9QUK6, UniProt: Q4G1L2 #2: タンパク質 | 分子量: 17392.793 Da / 分子数: 2 / 断片: UNP residues 19-160 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q9JHF9 #3: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #4: 糖 | ChemComp-NAG / Has protein modification | Y | |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 3.3 Å3/Da / 溶媒含有率: 62.69 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 / 詳細: 0.1 M Bicine, pH 7.5, 12% PEG10000 |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2014年11月5日 |
放射 | モノクロメーター: double crystal Si(111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.97918 Å / 相対比: 1 |
反射 | 解像度: 2.9→50 Å / Num. obs: 51785 / % possible obs: 99.6 % / 冗長度: 7.9 % / Rmerge(I) obs: 0.083 / Net I/av σ(I): 27.052 / Net I/σ(I): 8.7 |
反射 シェル | 解像度: 2.9→2.95 Å |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: PDB entry 2Z64 解像度: 2.91→48.81 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.886 / SU B: 45.049 / SU ML: 0.379 / 交差検証法: THROUGHOUT / ESU R: 1.964 / ESU R Free: 0.448 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 100.275 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.91→48.81 Å
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拘束条件 |
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