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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: 1gc1 | |||||||||
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タイトル | HIV-1 GP120 CORE COMPLEXED WITH CD4 AND A NEUTRALIZING HUMAN ANTIBODY | |||||||||
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![]() | Viral protein/receptor/Immune system / COMPLEX (HIV ENVELOPE PROTEIN-CD4-FAB) / HIV-1 EXTERIOR ENVELOPE GP120 / T-CELL SURFACE GLYCOPROTEIN CD4 / ANTIGEN-BINDING FRAGMENT OF HUMAN IMMUNOGLOBULIN 17B / GLYCOSYLATED PROTEIN / Viral protein-receptor-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 / Synthesis and processing of ENV and VPU / MHC class II protein binding / evasion of host immune response / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / Synthesis and processing of ENV and VPU / MHC class II protein binding / evasion of host immune response / 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 / actin filament organization / Assembly Of The HIV Virion / clathrin-coated endocytic vesicle membrane / Budding and maturation of HIV virion / 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 / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / early endosome / viral protein processing / cell adhesion / symbiont entry into host cell / positive regulation of protein phosphorylation / immune response / membrane raft / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / external side of plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / virion attachment to host cell / endoplasmic reticulum membrane / protein kinase binding / host cell plasma membrane / structural molecule activity / virion membrane / positive regulation of DNA-templated transcription / 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. / Robinson, J. / Sweet, R.W. / Sodroski, J. / Hendrickson, W.A. | |||||||||
![]() | ![]() 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 | ![]() | 208.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 166.2 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 | ![]() | 595 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 633.5 KB | 表示 | |
XML形式データ | ![]() | 24.3 KB | 表示 | |
CIF形式データ | ![]() | 39.3 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
-抗体 , 3種, 3分子 CLH
#2: 抗体 | 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 |
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#3: 抗体 | 分子量: 23368.818 Da / 分子数: 1 / 断片: ANTIGEN-BINDING FRAGMENT, FAB / 由来タイプ: 組換発現 詳細: MONOCLONAL ANTIBODY 17B BINDS TO A CD4-INDUCED SITE ON GP120 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: ![]() ![]() |
#4: 抗体 | 分子量: 24483.471 Da / 分子数: 1 / 断片: ANTIGEN-BINDING FRAGMENT, FAB / 由来タイプ: 組換発現 詳細: MONOCLONAL ANTIBODY 17B BINDS TO A CD4-INDUCED SITE ON GP120 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: ![]() ![]() |
-タンパク質 / 非ポリマー , 2種, 604分子 G![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: タンパク質 | 分子量: 35429.160 Da / 分子数: 1 / 断片: CORE 変異: (GARS) SUBSTITUTION AT THE N TERMINUS, GLY ALA GLY SUBSTITUTIONS FOR THE V1/V2 AND V3 LOOPS 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 METALLOTHIONEIN PROMOTER 遺伝子: env / 器官: OVARY / Variant: HXBC2 発現宿主: ![]() ![]() 参照: UniProt: P04578 |
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#7: 水 | ChemComp-HOH / |
-糖 , 2種, 11分子 ![](data/chem/img/NAG.gif)
#5: 多糖 | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose #6: 糖 | ChemComp-NAG / |
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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 Å3/Da / 溶媒含有率: 59 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 手法: 蒸気拡散法 / pH: 7 詳細: VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0. ...詳細: VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0.0075% SEAPREP AGAROSE, PH 6.4 OVER A RESERVOIR OF 0.35 M NACL, 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, PH 6.4, vapor diffusion PH範囲: 6.4-7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 37 ℃ / pH: 6.4 / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: Kwong, P.D., (1999) J. Biol. Chem., 274, 4115. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: FUJI / 検出器: IMAGE PLATE / 日付: 1996年8月1日 / 詳細: MIRRORS |
放射 | モノクロメーター: SILICON CRYSTAL / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 1.00614 Å / 相対比: 1 |
反射 | 解像度: 2.5→20 Å / Num. obs: 37724 / % possible obs: 86 % / Observed criterion σ(I): -0.5 / 冗長度: 3 % / Rsym value: 0.093 / Net I/σ(I): 9.17 |
反射 シェル | 解像度: 2.5→2.59 Å / 冗長度: 1.56 % / Mean I/σ(I) obs: 2.17 / Rsym value: 0.247 / % possible all: 62.8 |
反射 | *PLUS % possible obs: 86 % / Num. measured all: 113966 / Rmerge(I) obs: 0.093 |
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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 ENTRIES 1HIL, 1CDH AND 3CD4 解像度: 2.5→5 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 2
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原子変位パラメータ | Biso mean: 21 Å2
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Refine analyze | Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.5→5 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.5→2.58 Å / Total num. of bins used: 10
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Xplor file |
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ソフトウェア | *PLUS 名称: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS Rfactor Rfree: 0.3026 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS |