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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: 1g9n | |||||||||
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タイトル | HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B | |||||||||
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![]() | Viral protein/Immune system / COMPLEX (HIV ENVELOPE PROTEIN-CD4-FAB) / HIV-1 EXTERIOR ENVELOPE GP120 FROM CLINICAL PRIMARY ISOLATE / YU2 / T-CELL SURFACE GLYCOPROTEIN CD4 / ANTIGEN-BINDING FRAGMENT OF HUMAN IMMUNOGLOBULIN 17B / Viral protein-Immune system COMPLEX | |||||||||
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 / Dectin-2 family / 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 / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of establishment of T cell polarity / T cell activation / positive regulation of interleukin-2 production / 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 / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / early endosome / viral protein processing / cell adhesion / positive regulation of protein phosphorylation / immune response / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / virion attachment to host cell / 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 / membrane / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Kwong, P.D. / Wyatt, R. / Majeed, S. / Robinson, J. / Sweet, R.W. / Sodroski, J. / Hendrickson, W.A. | |||||||||
![]() | ![]() タイトル: Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. 著者: Kwong, P.D. / Wyatt, R. / Majeed, S. / Robinson, J. / Sweet, R.W. / Sodroski, J. / Hendrickson, W.A. #1: ![]() タイトル: Structure of an HIV GP120 Envelope Glycoprotein in Complex with the CD4 Receptor and a Neutralizing Human Antibody 著者: Kwong, P.D. / Wyatt, R. / Robinson, J. / Sweet, R.W. / Sodroski, J. / Hendrickson, W.A. | |||||||||
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 | ![]() | 208 KB | 表示 | ![]() |
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PDB形式 | ![]() | 163.3 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 | ![]() | 424.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 475.7 KB | 表示 | |
XML形式データ | ![]() | 27.1 KB | 表示 | |
CIF形式データ | ![]() | 41.6 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
-タンパク質 , 2種, 2分子 GC
#1: タンパク質 | 分子量: 34838.691 Da / 分子数: 1 / 断片: CORE / 変異: VARIABLE LOOPS SUBSTITUTED / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 属: Lentivirus / 株: CLADE B 解説: SECRETED FROM DROSOPHILA SCHNEIDER 2 LINES UNDER CONTROL OF AN INDUCIBLE METALL OTHIONEIN PROMOTER; Variant: PRIMARY ISOLATE YU2 発現宿主: ![]() ![]() 参照: UniProt: P35961 |
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#2: タンパク質 | 分子量: 20503.260 Da / 分子数: 1 / 断片: D1D2, N-TERMINAL TWO DOMAIN FRAGMENT / 変異: S184N, I185T / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: P01730 |
-抗体 , 2種, 2分子 LH
#3: 抗体 | 分子量: 23439.961 Da / 分子数: 1 / 断片: ANTIGEN-BINDING FRAGMENT, FAB / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 解説: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER 発現宿主: ![]() ![]() |
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#4: 抗体 | 分子量: 24525.578 Da / 分子数: 1 / 断片: ANTIGEN-BINDING FRAGMENT, FAB / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 解説: EPSTEIN-BARR VIRUS IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER 発現宿主: ![]() ![]() |
-糖 / 非ポリマー , 2種, 359分子 ![](data/chem/img/NAG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: 糖 | ChemComp-NAG / #6: 水 | ChemComp-HOH / | |
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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: 2.6 Å3/Da / 溶媒含有率: 53 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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: 5.9 詳細: VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (5 MG/ML IN 0.35 M NACL, 0.005 M TRIS CL PH 7.0) + 0.35 UL OF RESERVOIR (50 UL OF NA ACETATE pH 4.5 + 250 UL OF HAMPTON CRYSTAL SCREEN ...詳細: VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (5 MG/ML IN 0.35 M NACL, 0.005 M TRIS CL PH 7.0) + 0.35 UL OF RESERVOIR (50 UL OF NA ACETATE pH 4.5 + 250 UL OF HAMPTON CRYSTAL SCREEN REAGENT 18 + 126 UL OF ETHANOL + 292 UL OF WATER), pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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 4 / 検出器: CCD / 日付: 2000年4月26日 |
放射 | モノクロメーター: silicon 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: 0.9721 Å / 相対比: 1 |
反射 | 解像度: 2.9→20 Å / Num. all: 102604 / Num. obs: 23464 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 4.37 % / Biso Wilson estimate: 60.5 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 10.38 |
反射 シェル | 解像度: 2.9→3 Å / 冗長度: 3.3 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.33 / Num. unique all: 2315 / Rsym value: 0.439 / % possible all: 97.1 |
反射 シェル | *PLUS % possible obs: 97.1 % |
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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: ![]() 開始モデル: PDB ENTRY 1G9M 解像度: 2.9→20 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: Isotropic / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber 詳細: OVERALL ANISOTROPIC B VALUE CORRECTION APPLIED TO DATA DURING CNS REFINEMENT
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溶媒の処理 | 溶媒モデル: flat model / Bsol: 14.4408 Å2 / ksol: 0.217018 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 68.1 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.9→20 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.9→2.94 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 23
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Xplor file |
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ソフトウェア | *PLUS 名称: CNS / 分類: refinement | ||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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