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基本情報
登録情報 | データベース: PDB / ID: 3dno | ||||||
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タイトル | Molecular structure for the HIV-1 gp120 trimer in the CD4-bound state | ||||||
![]() | (HIV-1 envelope glycoprotein gp120) x 3 | ||||||
![]() | VIRAL PROTEIN / HIV-1 / ENVELOPE GLYCOPROTEIN / IMMUNODEFICIENCY VIRUS / gp120 / AIDS / Apoptosis / Cleavage on pair of basic residues / Envelope protein / Fusion protein / Host-virus interaction / Lipoprotein / Membrane / Palmitate / Viral immunoevasion / Virion | ||||||
機能・相同性 | ![]() Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 20 Å | ||||||
![]() | Borgnia, M.J. / Liu, J. / Bartesaghi, A. / Sapiro, G. / Subramaniam, S. | ||||||
![]() | ![]() 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. | ||||||
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構造の表示
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構造ビューア | 分子: ![]() ![]() |
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PDB形式 | ![]() | 140 KB | 表示 | ![]() |
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-関連構造データ
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質・ペプチド | 分子量: 4225.840 Da / 分子数: 3 / 断片: Core: Residues 90-124 / 由来タイプ: 組換発現 / 詳細: Human immunodeficiency virus type 1 由来: (組換発現) ![]() 株: isolate HXB2 group M subtype B, BaL / 遺伝子: env / 発現宿主: ![]() #2: タンパク質 | 分子量: 18570.014 Da / 分子数: 3 / 断片: Core: Residues 198-396 / 由来タイプ: 組換発現 / 詳細: Human immunodeficiency virus type 1 由来: (組換発現) ![]() 株: isolate HXB2 group M subtype B, BaL / 遺伝子: env / 発現宿主: ![]() #3: タンパク質 | 分子量: 9330.696 Da / 分子数: 3 / 断片: Core: Residues 410-492 / 由来タイプ: 組換発現 / 詳細: Human immunodeficiency virus type 1 由来: (組換発現) ![]() 株: isolate HXB2 group M subtype B, BaL / 遺伝子: env / 発現宿主: ![]() |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 |
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ウイルスについての詳細 | ホストのカテゴリ: VERTEBRATES / 単離: STRAIN / タイプ: VIRION | ||||||||||||
天然宿主 | 生物種: Homo sapiens / 株: SupT1-CCR5 CL.30 | ||||||||||||
緩衝液 | 名称: 0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA / pH: 7.2 / 詳細: 0.01 M Tris-HCl, 0.1 M NaCl, 1 mM EDTA | ||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||
試料支持 | 詳細: Home made holey-carbon | ||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK I / 凍結剤: ETHANE / 詳細: Ethane 77K 100%RH Vitrobot |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Tecnai Polara / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI POLARA 300 |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 34000 X / 最大 デフォーカス(公称値): 4000 nm / 最小 デフォーカス(公称値): 2000 nm / Cs: 2.2 mm |
試料ホルダ | 温度: 90 K / 傾斜角・最大: 70 ° / 傾斜角・最小: -70 ° |
撮影 | 電子線照射量: 80 e/Å2 / フィルム・検出器のモデル: GENERIC CCD |
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解析
EMソフトウェア |
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CTF補正 | 詳細: No CTF correction applied | ||||||||||||
対称性 | 点対称性: C3 (3回回転対称) | ||||||||||||
3次元再構成 | 手法: Tomographic reconstruction Weighted Back Projection / 解像度: 20 Å / ピクセルサイズ(公称値): 0.41 Å 詳細: IMOD was used for tomographic reconstruction. Programs developed in-house were used for alignment and classification of individual tomographic volumes. The final map is the average of ~4000 individual spikes. 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL / Target criteria: correlation coefficient 詳細: METHOD--Automatic. The coordinates for this entry and the two related entries 3DNL and 3DNN are based on fitting 1GC1 coordinates for the gp120 monomer deposited previously by Kwong et al in ...詳細: METHOD--Automatic. The coordinates for this entry and the two related entries 3DNL and 3DNN are based on fitting 1GC1 coordinates for the gp120 monomer deposited previously by Kwong et al in 1998 into the density map for the trimer derived by electron microscopy. Therefore, authors did not deposit new structure factors, and, any features such as unusual torsion angles are the same as in the 1GC1 coordinates. REFINEMENT PROTOCOL--rigid body | ||||||||||||
原子モデル構築 | PDB-ID: 1GC1 | ||||||||||||
精密化ステップ | サイクル: LAST
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