+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6b8o | ||||||
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タイトル | WT Ig-like V Domain with Phosphatidylserine | ||||||
要素 | Triggering receptor expressed on myeloid cells 2 | ||||||
キーワード | SIGNALING PROTEIN / Membrane receptor | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of high-density lipoprotein particle clearance / regulation of toll-like receptor 6 signaling pathway / positive regulation of complement activation, classical pathway / detection of lipoteichoic acid / regulation of macrophage inflammatory protein 1 alpha production / regulation of hippocampal neuron apoptotic process / regulation of plasma membrane bounded cell projection organization / positive regulation of inward rectifier potassium channel activity / positive regulation of C-C chemokine receptor CCR7 signaling pathway / positive regulation of CAMKK-AMPK signaling cascade ...positive regulation of high-density lipoprotein particle clearance / regulation of toll-like receptor 6 signaling pathway / positive regulation of complement activation, classical pathway / detection of lipoteichoic acid / regulation of macrophage inflammatory protein 1 alpha production / regulation of hippocampal neuron apoptotic process / regulation of plasma membrane bounded cell projection organization / positive regulation of inward rectifier potassium channel activity / positive regulation of C-C chemokine receptor CCR7 signaling pathway / positive regulation of CAMKK-AMPK signaling cascade / excitatory synapse pruning / positive regulation of CD40 signaling pathway / negative regulation of cell activation / detection of peptidoglycan / positive regulation of macrophage fusion / import into cell / sulfatide binding / positive regulation of engulfment of apoptotic cell / negative regulation of macrophage colony-stimulating factor signaling pathway / regulation of intracellular signal transduction / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / negative regulation of fat cell proliferation / lipoteichoic acid binding / positive regulation of establishment of protein localization / positive regulation of synapse pruning / microglial cell activation involved in immune response / negative regulation of toll-like receptor 2 signaling pathway / negative regulation of astrocyte activation / apolipoprotein A-I binding / respiratory burst after phagocytosis / positive regulation of low-density lipoprotein particle clearance / positive regulation of microglial cell migration / negative regulation of autophagic cell death / Other semaphorin interactions / detection of lipopolysaccharide / CXCL12-activated CXCR4 signaling pathway / negative regulation of p38MAPK cascade / high-density lipoprotein particle binding / very-low-density lipoprotein particle binding / negative regulation of neuroinflammatory response / negative regulation of toll-like receptor 4 signaling pathway / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of glial cell apoptotic process / regulation of resting membrane potential / microglial cell proliferation / negative regulation of NLRP3 inflammasome complex assembly / dendritic cell differentiation / complement-mediated synapse pruning / regulation of TOR signaling / low-density lipoprotein particle binding / positive regulation of microglial cell activation / amyloid-beta clearance by cellular catabolic process / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of phagocytosis, engulfment / phagocytosis, recognition / positive regulation of chemotaxis / cellular response to peptidoglycan / peptidoglycan binding / positive regulation of proteasomal protein catabolic process / positive regulation of amyloid-beta clearance / kinase activator activity / phosphatidylethanolamine binding / positive regulation of osteoclast differentiation / negative regulation of amyloid fibril formation / positive regulation of kinase activity / cellular response to lipid / apoptotic cell clearance / regulation of interleukin-6 production / dendritic spine maintenance / negative regulation of interleukin-1 beta production / negative regulation of sequestering of triglyceride / phagocytosis, engulfment / regulation of innate immune response / positive regulation of ATP biosynthetic process / pyroptotic inflammatory response / phosphatidylserine binding / negative regulation of cholesterol storage / regulation of cytokine production involved in inflammatory response / plasma membrane raft / lipid homeostasis / cellular response to lipoteichoic acid / lipoprotein particle binding / apolipoprotein binding / humoral immune response / positive regulation of interleukin-10 production / social behavior / regulation of lipid metabolic process / negative regulation of tumor necrosis factor production / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of TOR signaling / positive regulation of cholesterol efflux / response to axon injury / negative regulation of cytokine production involved in inflammatory response / negative regulation of canonical NF-kappaB signal transduction / positive regulation of phagocytosis / regulation of peptidyl-tyrosine phosphorylation / negative regulation of inflammatory response to antigenic stimulus / positive regulation of calcium-mediated signaling / negative regulation of autophagy / osteoclast differentiation 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.2 Å | ||||||
データ登録者 | Sudom, A. / Wang, Z. | ||||||
引用 | ジャーナル: J. Biol. Chem. / 年: 2018 タイトル: Molecular basis for the loss-of-function effects of the Alzheimer's disease-associated R47H variant of the immune receptor TREM2. 著者: Sudom, A. / Talreja, S. / Danao, J. / Bragg, E. / Kegel, R. / Min, X. / Richardson, J. / Zhang, Z. / Sharkov, N. / Marcora, E. / Thibault, S. / Bradley, J. / Wood, S. / Lim, A.C. / Chen, H. / ...著者: Sudom, A. / Talreja, S. / Danao, J. / Bragg, E. / Kegel, R. / Min, X. / Richardson, J. / Zhang, Z. / Sharkov, N. / Marcora, E. / Thibault, S. / Bradley, J. / Wood, S. / Lim, A.C. / Chen, H. / Wang, S. / Foltz, I.N. / Sambashivan, S. / Wang, Z. #1: ジャーナル: To Be Published タイトル: Structure of Ig-like V domain in complex with phosphatidylserine to 2.2 Angstrom resolution 著者: Sudom, A. / Wang, Z. / Min, X. | ||||||
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 | 6b8o.cif.gz | 152.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6b8o.ent.gz | 117.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6b8o.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 | 6b8o_validation.pdf.gz | 1.4 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6b8o_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | 6b8o_validation.xml.gz | 30.9 KB | 表示 | |
CIF形式データ | 6b8o_validation.cif.gz | 39.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/b8/6b8o ftp://data.pdbj.org/pub/pdb/validation_reports/b8/6b8o | 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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1 |
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単位格子 |
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-要素
-タンパク質 / 糖 , 2種, 12分子 ABCDEF
#1: タンパク質 | 分子量: 19138.254 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TREM2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9NZC2 #2: 糖 | ChemComp-NAG / |
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-非ポリマー , 5種, 113分子
#3: 化合物 | ChemComp-IOD / #4: 化合物 | ChemComp-SO4 / #5: 化合物 | ChemComp-EDO / #6: 化合物 | #7: 水 | ChemComp-HOH / | |
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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: 2.41 Å3/Da / 溶媒含有率: 49.01 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法 / 詳細: 0.2 M NaI, 1.6 M ammonium sulfate, 50 mM Tris 8.5 |
-データ収集
回折 | 平均測定温度: 80 K | ||||||||||||||||||||||||
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放射光源 | 由来: シンクロトロン / サイト: ALS / ビームライン: 5.0.2 / 波長: 1.00001 Å | ||||||||||||||||||||||||
検出器 | タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2017年7月28日 | ||||||||||||||||||||||||
放射 | 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: 1.00001 Å / 相対比: 1 | ||||||||||||||||||||||||
反射 | 解像度: 2.2→47.36 Å / Num. obs: 57469 / % possible obs: 100 % / 冗長度: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Net I/σ(I): 19.8 / Num. measured all: 752391 / Scaling rejects: 0 | ||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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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: 分子置換 開始モデル: 5UD7 解像度: 2.2→47.36 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.77 / SU ML: 0.142 / SU R Cruickshank DPI: 0.201 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.184 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 148.23 Å2 / Biso mean: 52.028 Å2 / Biso min: 19.21 Å2
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精密化ステップ | サイクル: final / 解像度: 2.2→47.36 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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