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基本情報
登録情報 | データベース: PDB / ID: 2qad | ||||||
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タイトル | Structure of tyrosine-sulfated 412d antibody complexed with HIV-1 YU2 gp120 and CD4 | ||||||
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![]() | viral protein/immune system / 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 / immunoglobulin complex / regulation of T cell activation / extracellular matrix structural constituent / T cell receptor complex / 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 / immunoglobulin mediated immune response / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / 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 calcium-mediated signaling / positive regulation of interleukin-2 production / protein tyrosine kinase binding / host cell endosome membrane / clathrin-coated endocytic vesicle membrane / antigen binding / Vpu mediated degradation of CD4 / calcium-mediated signaling / transmembrane signaling receptor activity / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of T cell activation / Clathrin-mediated endocytosis / virus receptor activity / Downstream TCR signaling / MHC class II protein complex binding / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / clathrin-dependent endocytosis of virus by host cell / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / blood microparticle / cell surface receptor signaling pathway / positive regulation of viral entry into host cell / early endosome / viral protein processing / cell adhesion / positive regulation of protein phosphorylation / membrane raft / immune response / 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 / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / virion attachment to host cell / protein kinase binding / apoptotic process / enzyme binding / structural molecule activity / host cell plasma membrane / virion membrane / 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 | ![]() ![]() ![]() | ||||||
![]() | Huang, C.-C. / Tang, M. / Robinson, J. / Wyatt, R. / Kwong, P.D. | ||||||
![]() | ![]() タイトル: Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4 著者: Huang, C.-C. / Lam, S.N. / Acharya, P. / Tang, M. / Xiang, S.-H. / Hussan, S.S. / Stanfield, R.L. / Robinson, J. / Sodroski, J. / Wilson, I.A. / Wyatt, R. / Bewley, C.A. / Kwong, P.D. | ||||||
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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PDBx/mmCIF形式 | ![]() | 778.8 KB | 表示 | ![]() |
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PDB形式 | ![]() | 651.8 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-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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2 | ![]()
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3 |
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単位格子 |
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詳細 | this entry contains the crystallographic asymmetric unit which consists of two gp120/cd4/412d complexes. chain A, B, C, and D form one complex, and chain E, F, G, and H form the other. |
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要素
-タンパク質 , 2種, 4分子 AEBF
#1: タンパク質 | 分子量: 36062.059 Da / 分子数: 2 / 断片: CORE WITH V3 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 属: Lentivirus / 株: YU2 / 遺伝子: env / プラスミド: CMVR / 細胞株 (発現宿主): EMBRYONIC CELL LINE 293 / 発現宿主: ![]() #2: タンパク質 | 分子量: 20129.896 Da / 分子数: 2 / 断片: D1D2, IG-LIKE V-TYPE AND IG-LIKE C2-TYPE 1 DOMAINS / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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-抗体 , 2種, 4分子 CGDH
#3: 抗体 | 分子量: 23483.066 Da / 分子数: 2 / 断片: FAB, ANTIGEN-BINDING FRAGMENT / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() 株 (発現宿主): Epstein-barr virus / 参照: UniProt: Q6GMX8 #4: 抗体 | 分子量: 24839.684 Da / 分子数: 2 / 断片: FAB, ANTIGEN-BINDING FRAGMENT / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() 株 (発現宿主): Epstein-barr virus / 参照: UniProt: A4F255 |
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-糖 , 1種, 31分子 ![](data/chem/img/NAG.gif)
#5: 糖 | ChemComp-NAG / |
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-非ポリマー , 2種, 11分子 ![](data/chem/img/MLA.gif)
![](data/chem/img/EDO.gif)
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#6: 化合物 | ChemComp-MLA / #7: 化合物 | ChemComp-EDO / |
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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: 3.02 Å3/Da / 溶媒含有率: 59.27 % |
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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: 6.5 詳細: 17-19% polyethylene glycol (PEG) 1500, 0.1 M Na cacodylate pH 6.5, 0.2 M Na malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: MARRESEARCH / 検出器: CCD / 日付: 2004年4月20日 |
放射 | モノクロメーター: Si (220) / 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: 3.3→50 Å / Num. obs: 25816 / % possible obs: 67.8 % / Observed criterion σ(I): -3 / 冗長度: 3.1 % / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 9.1 |
反射 シェル | 解像度: 3.3→3.42 Å / 冗長度: 1.7 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 1.3 / Num. unique all: 595 / % possible all: 16.2 |
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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: YU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG 解像度: 3.3→20 Å / Isotropic thermal model: overall / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber 詳細: TLS refinement was performed with PHENIX. The anisotropic B-factor in ANISOU records is the total B-factor (B_tls + B_individual). The isotropic equivalent B-factor in ATOM records is the ...詳細: TLS refinement was performed with PHENIX. The anisotropic B-factor in ANISOU records is the total B-factor (B_tls + B_individual). The isotropic equivalent B-factor in ATOM records is the mean of the trace of the ANISOU matrix divided by 10000 and multiplied by 8*pi^2 and represents the isotropic equivalent of the total B-factor (B_tls + B_individual). To obtain the individual B-factors, one needs to compute the TLS component (B_tls) using the TLS records in the PDB file header and then subtract it from the total B-factors (on the ANISOU records).
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原子変位パラメータ | Biso mean: 156 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: 3.3→20 Å
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拘束条件 |
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