+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3ul8 | ||||||||||||
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タイトル | Crystal structure of the TV3 mutant V134L | ||||||||||||
要素 | Toll-like receptor 4, Variable lymphocyte receptor BToll様受容体 | ||||||||||||
キーワード | IMMUNE SYSTEM (免疫系) / LRR / protein binding (タンパク質) / MD-2 / extracellular matrix (細胞外マトリックス) | ||||||||||||
機能・相同性 | 機能・相同性情報 nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / detection of fungus / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / lipopolysaccharide immune receptor activity / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / lipopolysaccharide receptor complex / positive regulation of matrix metallopeptidase secretion / detection of lipopolysaccharide / regulation of dendritic cell cytokine production ...nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / detection of fungus / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / lipopolysaccharide immune receptor activity / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / lipopolysaccharide receptor complex / positive regulation of matrix metallopeptidase secretion / detection of lipopolysaccharide / regulation of dendritic cell cytokine production / intestinal epithelial structure maintenance / MyD88-independent TLR4 cascade / negative regulation of interleukin-23 production / TRIF-mediated programmed cell death / I-kappaB phosphorylation / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / wound healing involved in inflammatory response / Caspase activation via Death Receptors in the presence of ligand / B cell proliferation involved in immune response / nucleotide-binding oligomerization domain containing 1 signaling pathway / Toll Like Receptor 4 (TLR4) Cascade / positive regulation of interleukin-1 production / マクロファージ / Regulation of TLR by endogenous ligand / microglia differentiation / astrocyte development / TRIF-dependent toll-like receptor signaling pathway / positive regulation of macrophage activation / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of interleukin-17 production / positive regulation of cytokine production involved in inflammatory response / NADP+ nucleosidase activity / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of MHC class II biosynthetic process / positive regulation of platelet activation / positive regulation of chemokine (C-X-C motif) ligand 2 production / MyD88 deficiency (TLR2/4) / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of cold-induced thermogenesis / positive regulation of macrophage cytokine production / MyD88-dependent toll-like receptor signaling pathway / positive regulation of reactive oxygen species biosynthetic process / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / Toll様受容体 / phagocytic cup / positive regulation of NLRP3 inflammasome complex assembly / T-helper 1 type immune response / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / negative regulation of osteoclast differentiation / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of interferon-alpha production / cellular response to lipoteichoic acid / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / 食作用 / positive regulation of B cell proliferation / positive regulation of chemokine production / JNK cascade / lipopolysaccharide-mediated signaling pathway / ERK1 and ERK2 cascade / ruffle / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / nitric oxide biosynthetic process / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of smooth muscle cell proliferation / positive regulation of JNK cascade / Heme signaling / positive regulation of MAP kinase activity / negative regulation of ERK1 and ERK2 cascade / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / cellular response to amyloid-beta / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / transmembrane signaling receptor activity / positive regulation of tumor necrosis factor production / signaling receptor activity / 遺伝子発現 / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / ER-Phagosome pathway / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) Eptatretus burgeri (ヌタウナギ) | ||||||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.5 Å | ||||||||||||
データ登録者 | Kim, H.J. / Cheong, H.K. / Jeon, Y.H. | ||||||||||||
引用 | ジャーナル: Plos One / 年: 2012 タイトル: Structure-Based Rational Design of a Toll-like Receptor 4 (TLR4) Decoy Receptor with High Binding Affinity for a Target Protein. 著者: Han, J. / Kim, H.J. / Lee, S.C. / Hong, S. / Park, K. / Jeon, Y.H. / Kim, D. / Cheong, H.K. / Kim, H.S. | ||||||||||||
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 | 3ul8.cif.gz | 73.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3ul8.ent.gz | 51.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3ul8.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/ul/3ul8 ftp://data.pdbj.org/pub/pdb/validation_reports/ul/3ul8 | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
-タンパク質 , 1種, 1分子 A
#1: タンパク質 | 分子量: 31400.982 Da / 分子数: 1 / 断片: UNP RESIDUES 27-228, UNP RESIDUES 126-199 / 変異: V134L / 由来タイプ: 組換発現 詳細: THE FUSION PROTEIN OF TLR4 (UNP RESIDUES 27-228) AND VLRB (UNP RESIDUES 126-199) 由来: (組換発現) Homo sapiens (ヒト), (組換発現) Eptatretus burgeri (ヌタウナギ) 遺伝子: TLR4, VLRB 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: O00206, UniProt: Q4G1L2 |
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-糖 , 3種, 3分子
#2: 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 |
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#3: 糖 | ChemComp-NAG / |
#4: 糖 | ChemComp-FUL / |
-非ポリマー , 2種, 33分子
#5: 化合物 | ChemComp-SO4 / |
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#6: 水 | ChemComp-HOH / |
-詳細
配列の詳細 | THE FUSION PROTEIN OF TLR4 (UNP RESIDUES 27-228) AND VLRB.61 (UNP RESIDUES 126-199) |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.49 Å3/Da / 溶媒含有率: 50.7 % |
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結晶化 | 温度: 296 K / 手法: 蒸気拡散法 / pH: 5.5 詳細: 0.1M Bis-Tris(pH5.5), 36% PEG 1000, 0.2M Lithium sulfate, VAPOR DIFFUSION, temperature 296K |
-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: シンクロトロン / サイト: PAL/PLS / ビームライン: 4A / 波長: 1 Å |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2010年4月23日 |
放射 | モノクロメーター: double crystal / 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: 1 Å / 相対比: 1 |
反射 | 解像度: 2.45→50 Å / Num. obs: 11557 / % possible obs: 94.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
反射 シェル | 解像度: 2.5→2.59 Å |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 2Z62 解像度: 2.5→50 Å / 交差検証法: THROUGHOUT / 立体化学のターゲット値: maximum likelihood
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精密化ステップ | サイクル: LAST / 解像度: 2.5→50 Å
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LS精密化 シェル | 解像度: 2.5→2.59 Å |