+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1rzj | |||||||||
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タイトル | HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B | |||||||||
要素 |
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キーワード | Viral protein/Immune system / COMPLEX (HIV ENVELOPE PROTEIN-CD4-FAB) / HIV-1 EXTERIOR ENVELOPE GP120 FROM LABORATORY-ADAPTED ISOLATE / HXBC2 / SURFACE T-CELL GLYCOPROTEIN CD4 / ANTIGEN-BINDING FRAGMENT OF HUMAN IMMUNOGLOBULIN 17B / Viral protein-Immune system COMPLEX | |||||||||
機能・相同性 | 機能・相同性情報 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 / interleukin-15-mediated signaling pathway / regulation of T cell activation ...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 / interleukin-15-mediated signaling pathway / regulation of T cell activation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of monocyte differentiation / positive regulation of kinase activity / Nef Mediated CD4 Down-regulation / Alpha-defensins / 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 / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / host cell endosome membrane / T cell activation / actin filament organization / Vpu mediated degradation of CD4 / calcium-mediated signaling / Assembly Of The HIV Virion / clathrin-coated endocytic vesicle membrane / Budding and maturation of HIV virion / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of T cell activation / transmembrane signaling receptor activity / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / MHC class II protein complex binding / Clathrin-mediated endocytosis / signaling receptor activity / virus 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 ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / early endosome / cell surface receptor signaling pathway / viral protein processing / cell adhesion / immune response / symbiont entry into host cell / positive regulation of protein phosphorylation / 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 / endoplasmic reticulum membrane / virion attachment to host cell / apoptotic process / protein kinase binding / host cell plasma membrane / positive regulation of DNA-templated transcription / structural molecule activity / 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 | Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) Homo sapiens (ヒト) | |||||||||
手法 | X線回折 / シンクロトロン / THIS DEPOSIT IS the re-refinement of previously determined 1G9M structure / 解像度: 2.2 Å | |||||||||
データ登録者 | Huang, C.C. / Venturi, M. / Majeed, S. / Moore, M.J. / Phogat, S. / Zhang, M.-Y. / Dimitrov, D.S. / Hendrickson, W.A. / Robinson, J. / Sodroski, J. ...Huang, C.C. / Venturi, M. / Majeed, S. / Moore, M.J. / Phogat, S. / Zhang, M.-Y. / Dimitrov, D.S. / Hendrickson, W.A. / Robinson, J. / Sodroski, J. / Wyatt, R. / Choe, H. / Farzan, M. / Kwong, P.D. | |||||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2004 タイトル: Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120 著者: Huang, C.C. / Venturi, M. / Majeed, S. / Moore, M.J. / Phogat, S. / Zhang, M.-Y. / Dimitrov, D.S. / Hendrickson, W.A. / Robinson, J. / Sodroski, J. / Wyatt, R. / Choe, H. / Farzan, M. / Kwong, P.D. #1: ジャーナル: Structure / 年: 2000 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. | |||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1rzj.cif.gz | 218.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1rzj.ent.gz | 169.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1rzj.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 1rzj_validation.pdf.gz | 939.7 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1rzj_full_validation.pdf.gz | 973.9 KB | 表示 | |
XML形式データ | 1rzj_validation.xml.gz | 47.7 KB | 表示 | |
CIF形式データ | 1rzj_validation.cif.gz | 68 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/rz/1rzj ftp://data.pdbj.org/pub/pdb/validation_reports/rz/1rzj | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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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: 35429.094 Da / 分子数: 1 / 断片: CORE / 変異: VARIABLE LOOPS SUBSTITUTED / 由来タイプ: 組換発現 / 詳細: part of Envelope polyprotein GP160 由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス) 属: Lentivirus / 株: CLADE B 解説: SECRETED FROM DROSOPHILA SCHNEIDER 2 LINES UNDER CONTROL OF AN INDUCIBLE METALLOTHIONEIN PROMOTER Variant: LABORATORY-ADAPTED ISOLATE HXBC2 発現宿主: Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: P04578 |
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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) Homo sapiens (ヒト) / Cell (発現宿主): OVARY CELLS (CHO) 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 参照: UniProt: P01730 |
-抗体 , 2種, 2分子 LH
#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) Homo sapiens (ヒト) / 属 (発現宿主): Lymphocryptovirus Cell (発現宿主): IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER 発現宿主: Human herpesvirus 4 (ヘルペスウイルス) |
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#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) Homo sapiens (ヒト) / 属 (発現宿主): Lymphocryptovirus Cell (発現宿主): IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER 発現宿主: Human herpesvirus 4 (ヘルペスウイルス) |
-糖 , 2種, 14分子
#5: 多糖 | #6: 糖 | ChemComp-NAG / |
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-非ポリマー , 2種, 587分子
#7: 化合物 | ChemComp-IPA / |
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#8: 水 | ChemComp-HOH / |
-詳細
Has protein modification | Y |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.8 Å3/Da / 溶媒含有率: 55.3 % | |||||||||||||||||||||||||||||||||||
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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: 6.4 詳細: 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 ...詳細: 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, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
結晶化 | *PLUS pH: 7 / 手法: 蒸気拡散法, ハンギングドロップ法 | |||||||||||||||||||||||||||||||||||
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: シンクロトロン / サイト: NSLS / ビームライン: X4A / 波長: 0.97953 Å |
検出器 | タイプ: FUJI / 検出器: IMAGE PLATE / 日付: 1996年5月25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: 0.97953 Å / 相対比: 1 |
反射 | 解像度: 2.2→20 Å / Num. all: 56183 / Observed criterion σ(I): -0.35 / Biso Wilson estimate: 4.7 Å2 |
反射 シェル | 解像度: 2.2→2.28 Å / % possible all: 66.3 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: THIS DEPOSIT IS the re-refinement of previously determined 1G9M structure 解像度: 2.2→19.81 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 230514.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 43.0646 Å2 / ksol: 0.313979 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 31 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: 2.2→19.81 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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拘束条件 | *PLUS
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