+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-5020 | |||||||||
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タイトル | Molecular Structure of the Native HIV-1 gp120 trimer bound to CD4 and 17b: Spike region | |||||||||
マップデータ | CD4 and 17b-bound HIV-1 BaL spike | |||||||||
試料 |
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キーワード | HIV-1 / envelope glycoprotein. immunodeficiency virus / gp120 | |||||||||
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 / 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 / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / early endosome / viral protein processing / cell adhesion / symbiont entry into host cell / 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 / membrane / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | envelope glycoprotein (unknown) | |||||||||
手法 | サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 20.0 Å | |||||||||
データ登録者 | Bartesaghi A / Borgnia M / Liu J / Sapiro G / Subramaniam S | |||||||||
引用 | ジャーナル: Nature / 年: 2008 タイトル: Molecular architecture of native HIV-1 gp120 trimers. 著者: Jun Liu / Alberto Bartesaghi / Mario J Borgnia / Guillermo Sapiro / Sriram Subramaniam / 要旨: The envelope glycoproteins (Env) of human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate virus binding to the cell surface receptor CD4 on target cells to initiate infection. ...The envelope glycoproteins (Env) of human and simian immunodeficiency viruses (HIV and SIV, respectively) mediate virus binding to the cell surface receptor CD4 on target cells to initiate infection. Env is a heterodimer of a transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120), and forms trimers on the surface of the viral membrane. Using cryo-electron tomography combined with three-dimensional image classification and averaging, we report the three-dimensional structures of trimeric Env displayed on native HIV-1 in the unliganded state, in complex with the broadly neutralizing antibody b12 and in a ternary complex with CD4 and the 17b antibody. By fitting the known crystal structures of the monomeric gp120 core in the b12- and CD4/17b-bound conformations into the density maps derived by electron tomography, we derive molecular models for the native HIV-1 gp120 trimer in unliganded and CD4-bound states. We demonstrate that CD4 binding results in a major reorganization of the Env trimer, causing an outward rotation and displacement of each gp120 monomer. This appears to be coupled with a rearrangement of the gp41 region along the central axis of the trimer, leading to closer contact between the viral and target cell membranes. Our findings elucidate the structure and conformational changes of trimeric HIV-1 gp120 relevant to antibody neutralization and attachment to target cells. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_5020.map.gz | 188.7 KB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-5020-v30.xml emd-5020.xml | 9.9 KB 9.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_5020_1.jpg | 576 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-5020 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5020 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_5020_validation.pdf.gz | 285.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_5020_full_validation.pdf.gz | 285.2 KB | 表示 | |
XML形式データ | emd_5020_validation.xml.gz | 5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5020 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5020 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_5020.map.gz / 形式: CCP4 / 大きさ: 3.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | CD4 and 17b-bound HIV-1 BaL spike | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 4.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : HIV-1 BaL virus
全体 | 名称: HIV-1 BaL virus |
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要素 |
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-超分子 #1000: HIV-1 BaL virus
超分子 | 名称: HIV-1 BaL virus / タイプ: sample / ID: 1000 詳細: Structures determined by cryo-electron tomography combined with 3D averaging Number unique components: 1 |
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-超分子 #1: envelope glycoprotein
超分子 | 名称: envelope glycoprotein / タイプ: virus / ID: 1 / Name.synonym: envelope glycoprotein / 生物種: envelope glycoprotein / データベース: NCBI / ウイルスタイプ: VIRION / ウイルス・単離状態: STRAIN / ウイルス・エンベロープ: Yes / ウイルス・中空状態: No / Syn species name: envelope glycoprotein |
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宿主 | 生物種: Homo sapiens (ヒト) / 別称: VERTEBRATES |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | サブトモグラム平均法 |
-試料調製
緩衝液 | pH: 7.2 / 詳細: 0.01 M Tris, 0.1 M NaCl, 1 mM EDTA |
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グリッド | 詳細: home-made holey carbon |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 77 K / 装置: OTHER / 詳細: Vitrification instrument: Vitrobot / 手法: Blot and plunge |
-電子顕微鏡法
顕微鏡 | FEI POLARA 300 |
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温度 | 平均: 77 K |
特殊光学系 | エネルギーフィルター - 名称: Gatan エネルギーフィルター - エネルギー下限: 0.0 eV エネルギーフィルター - エネルギー上限: 20.0 eV |
撮影 | カテゴリ: CCD / フィルム・検出器のモデル: GENERIC CCD / 平均電子線量: 80 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.2 mm / 最大 デフォーカス(公称値): 4.0 µm / 最小 デフォーカス(公称値): 2.0 µm / 倍率(公称値): 34000 |
試料ステージ | 試料ホルダー: Cartridge / 試料ホルダーモデル: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 ° |
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
-画像解析
詳細 | Average number of tilts used in the 3D reconstructions: 400. Average tomographic tilt angle increment: 1. |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 20.0 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: IMOD and in-house procedures |