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基本情報
登録情報 | データベース: PDB / ID: 4jm2 | |||||||||
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タイトル | Crystal Structure of PGT 135 Fab in Complex with gp120 Core Protein from HIV-1 Strain JR-FL Bound to CD4 and 17b Fab | |||||||||
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![]() | IMMUNE SYSTEM/VIRAL PROTEIN / Immunoglobulin Fold / IMMUNE SYSTEM-VIRAL PROTEIN 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 / 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 / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Kong, L. / Wilson, I.A. | |||||||||
![]() | ![]() タイトル: Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120. 著者: Leopold Kong / Jeong Hyun Lee / Katie J Doores / Charles D Murin / Jean-Philippe Julien / Ryan McBride / Yan Liu / Andre Marozsan / Albert Cupo / Per-Johan Klasse / Simon Hoffenberg / Michael ...著者: Leopold Kong / Jeong Hyun Lee / Katie J Doores / Charles D Murin / Jean-Philippe Julien / Ryan McBride / Yan Liu / Andre Marozsan / Albert Cupo / Per-Johan Klasse / Simon Hoffenberg / Michael Caulfield / C Richter King / Yuanzi Hua / Khoa M Le / Reza Khayat / Marc C Deller / Thomas Clayton / Henry Tien / Ten Feizi / Rogier W Sanders / James C Paulson / John P Moore / Robyn L Stanfield / Dennis R Burton / Andrew B Ward / Ian A Wilson / ![]() 要旨: A substantial proportion of the broadly neutralizing antibodies (bnAbs) identified in certain HIV-infected donors recognize glycan-dependent epitopes on HIV-1 gp120. Here we elucidate how the bnAb ...A substantial proportion of the broadly neutralizing antibodies (bnAbs) identified in certain HIV-infected donors recognize glycan-dependent epitopes on HIV-1 gp120. Here we elucidate how the bnAb PGT 135 binds its Asn332 glycan-dependent epitope from its 3.1-Å crystal structure with gp120, CD4 and Fab 17b. PGT 135 interacts with glycans at Asn332, Asn392 and Asn386, using long CDR loops H1 and H3 to penetrate the glycan shield and access the gp120 protein surface. EM reveals that PGT 135 can accommodate the conformational and chemical diversity of gp120 glycans by altering its angle of engagement. Combined structural studies of PGT 135, PGT 128 and 2G12 show that this Asn332-dependent antigenic region is highly accessible and much more extensive than initially appreciated, which allows for multiple binding modes and varied angles of approach; thereby it represents a supersite of vulnerability for antibody neutralization. | |||||||||
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 | ![]() | 283.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 230.6 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 | ![]() | 1.5 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.6 MB | 表示 | |
XML形式データ | ![]() | 58.8 KB | 表示 | |
CIF形式データ | ![]() | 78.9 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 EF
#5: タンパク質 | 分子量: 35991.883 Da / 分子数: 1 / 断片: core with mini V3 loop / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 株: JRFL / 細胞株 (発現宿主): HEK 293S / 発現宿主: ![]() |
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#6: タンパク質 | 分子量: 20503.260 Da / 分子数: 1 断片: Ig-like V-type and C2-type 1 domains (UNP residues 26-208) 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
-抗体 , 4種, 4分子 ABCD
#1: 抗体 | 分子量: 25575.814 Da / 分子数: 1 / 断片: Fab / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() |
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#2: 抗体 | 分子量: 23795.467 Da / 分子数: 1 / 断片: Fab / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() |
#3: 抗体 | 分子量: 23399.898 Da / 分子数: 1 / 断片: Fab / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() |
#4: 抗体 | 分子量: 24457.387 Da / 分子数: 1 / 断片: Fab / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() |
-糖 , 4種, 9分子 ![](data/chem/img/NAG.gif)
#7: 多糖 | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#8: 多糖 | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#9: 多糖 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#11: 糖 | ChemComp-NAG / |
-非ポリマー , 2種, 2分子 ![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#10: 化合物 | ChemComp-PG4 / |
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#12: 水 | ChemComp-HOH / |
-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: 2.79 Å3/Da / 溶媒含有率: 55.93 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 詳細: 20% PEG2000, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, SITTING 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: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2011年10月2日 |
放射 | モノクロメーター: liquid N2 cooled double crystal Si(111) 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: 3.1→43.6 Å / Num. all: 30862 / Num. obs: 30862 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 3.7 % / Biso Wilson estimate: 105 Å2 / Rsym value: 0.06 / Net I/σ(I): 16.9 |
反射 シェル | 解像度: 3.1→3.2 Å / 冗長度: 3.3 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 2771 / Rsym value: 0.6 / % possible all: 98.8 |
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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: ![]()
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溶媒の処理 | 減衰半径: 0.83 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 77.33 Å2 / ksol: 0.287 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ |
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精密化ステップ | サイクル: LAST / 解像度: 3.1→43.578 Å
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拘束条件 |
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LS精密化 シェル |
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