+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 1rzj | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B | |||||||||
![]() |
| |||||||||
![]() | 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 | ![]() helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / response to methamphetamine hydrochloride / maintenance of protein location in cell / cellular response to ionomycin / T cell selection / Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / MHC class II protein binding ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / response to methamphetamine hydrochloride / maintenance of protein location in cell / cellular response to ionomycin / T cell selection / Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / MHC class II protein binding / positive regulation of kinase activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of establishment of T cell polarity / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / response to vitamin D / regulation of T cell activation / extracellular matrix structural constituent / Other interleukin signaling / T cell receptor complex / enzyme-linked receptor protein signaling pathway / Dectin-2 family / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of calcium ion transport into cytosol / positive regulation of protein kinase activity / regulation of calcium ion transport / Generation of second messenger molecules / macrophage differentiation / T cell differentiation / immunoglobulin binding / Co-inhibition by PD-1 / Binding and entry of HIV virion / coreceptor activity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / cell surface receptor protein tyrosine kinase signaling pathway / host cell endosome membrane / actin filament organization / Vpu mediated degradation of CD4 / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / Assembly Of The HIV Virion / Budding and maturation of HIV virion / MHC class II protein complex binding / transmembrane signaling receptor activity / positive regulation of protein phosphorylation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / response to estradiol / signaling receptor activity / Clathrin-mediated endocytosis / virus receptor activity / response to ethanol / defense response to Gram-negative bacterium / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / positive regulation of viral entry into host cell / early endosome / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / cell adhesion / positive regulation of MAPK cascade / viral protein processing / immune response / membrane raft / endoplasmic reticulum lumen / symbiont entry into host cell / external side of plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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 | ![]() ![]() | |||||||||
![]() | 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. | |||||||||
![]() | ![]() 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: ![]() 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 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 218.2 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 169.5 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 | ![]() | 939.7 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 973.9 KB | 表示 | |
XML形式データ | ![]() | 47.7 KB | 表示 | |
CIF形式データ | ![]() | 68 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
単位格子 |
|
-
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) ![]() ![]() 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: ![]() ![]() 参照: UniProt: P04578 |
---|---|
#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: 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) ![]() Cell (発現宿主): IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER 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) ![]() Cell (発現宿主): IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER 発現宿主: ![]() |
-糖 , 2種, 14分子 
#5: 多糖 | #6: 糖 | ChemComp-NAG / |
---|
-非ポリマー , 2種, 587分子 


#7: 化合物 | ChemComp-IPA / |
---|---|
#8: 水 | ChemComp-HOH / |
-詳細
Has protein modification | Y |
---|
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 2.8 Å3/Da / 溶媒含有率: 55.3 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-データ収集
回折 | 平均測定温度: 100 K |
---|---|
放射光源 | 由来: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.2→19.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
|