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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 6l1y | ||||||
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タイトル | structure of gp120/CD4 with a non-canonical surface | ||||||
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![]() | PROTEIN BINDING / HIV / gp120 / CD4 receptor | ||||||
機能・相同性 | ![]() helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / positive regulation of kinase activity / regulation of T cell activation / T cell receptor complex / extracellular matrix structural constituent / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / positive regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / positive regulation of interleukin-2 production / viral process / protein tyrosine kinase binding / host cell endosome membrane / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / positive regulation of T cell activation / MHC class II protein complex binding / Clathrin-mediated endocytosis / virus receptor activity / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / membrane => GO:0016020 / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / early endosome / cell adhesion / positive regulation of protein phosphorylation / immune response / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / lipid binding / viral envelope / endoplasmic reticulum membrane / protein kinase binding / host cell plasma membrane / structural molecule activity / positive regulation of DNA-templated transcription / virion membrane / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Liu, X. / Ning, W. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: A non-canonical binding interface in the crystal structure of HIV-1 gp120 core in complex with CD4. 著者: Duan, L.W. / Zhang, H. / Zhao, M.T. / Sun, J.X. / Chen, W.L. / Lin, J.P. / Liu, X.Q. | ||||||
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 | ![]() | 123.5 KB | 表示 | ![]() |
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PDB形式 | ![]() | 92 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 | ![]() | 2.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2.2 MB | 表示 | |
XML形式データ | ![]() | 22.6 KB | 表示 | |
CIF形式データ | ![]() | 31.5 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 3tgtS S: 精密化の開始モデル |
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類似構造データ |
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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: 43340.457 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 発現宿主: Insect expression vector pBlueBacmsGCA1His (その他) 参照: UniProt: G4XFJ5*PLUS | ||||||
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#2: タンパク質 | 分子量: 19654.334 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: Insect expression vector pBlueBacmsGCA1His (その他) 参照: UniProt: P01730 | ||||||
#3: 糖 | ChemComp-NAG / #4: 化合物 | ChemComp-EPE / | #5: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | |
-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: 2.78 Å3/Da / 溶媒含有率: 55.68 % |
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結晶化 | 温度: 293 K / 手法: 蒸発脱水法 / pH: 7.4 詳細: 0.1 M HEPES sodium, pH 7.4, 11% PEG 4000 and 10% 2-propanol |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: ![]() ![]() |
検出器 | タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2013年10月25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: 0.9792 Å / 相対比: 1 |
反射 | 解像度: 2.469→50 Å / Num. obs: 21690 / % possible obs: 95.6 % / 冗長度: 3 % / Biso Wilson estimate: 49.6 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.03 / Net I/σ(I): 21.6 |
反射 シェル | 解像度: 2.47→2.49 Å / 冗長度: 2.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 1803 / Rsym value: 0.32 / % possible all: 96.8 |
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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: 3TGT 解像度: 2.469→33.815 Å / SU ML: 0.37 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 30.01
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 117.59 Å2 / Biso mean: 49.87 Å2 / Biso min: 22.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 2.469→33.815 Å
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拘束条件 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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