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基本情報
登録情報 | データベース: EMDB / ID: EMD-1247 | |||||||||
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タイトル | Distribution and three-dimensional structure of AIDS virus envelope spikes. | |||||||||
![]() | 3D map of SIVmac239 viral membrane. It is acquired by subtracting the 3D averaged volume of "top/bottom view" spikes from averaged volume of the "side view" spikes (supplementary method of the reference) . Author's threshold 2.25. It should be loaded together with the associated SIVmac239 envelope spike map (SIVmac239_Env_spike.map, EMD-1246, author's threshold 2.65 ). | |||||||||
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生物種 | ![]() | |||||||||
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: 32.0 Å | |||||||||
![]() | Zhu P / Liu J / Bess J / Chertova E / Lifson JD / Grise H / Ofek GA / Taylor KA / Roux KH | |||||||||
![]() | ![]() タイトル: Distribution and three-dimensional structure of AIDS virus envelope spikes. 著者: Ping Zhu / Jun Liu / Julian Bess / Elena Chertova / Jeffrey D Lifson / Henry Grisé / Gilad A Ofek / Kenneth A Taylor / Kenneth H Roux / ![]() 要旨: Envelope glycoprotein (Env) spikes on AIDS retroviruses initiate infection of host cells and are therefore targets for vaccine development. Though crystal structures for partial Env subunits are ...Envelope glycoprotein (Env) spikes on AIDS retroviruses initiate infection of host cells and are therefore targets for vaccine development. Though crystal structures for partial Env subunits are known, the structure and distribution of native Env spikes on virions is obscure. We applied cryoelectron microscopy tomography to define ultrastructural details of spikes. Virions of wild-type human immunodeficiency virus 1 (HIV-1) and a mutant simian immunodeficiency virus (SIV) had approximately 14 and approximately 73 spikes per particle, respectively, with some clustering of HIV-1 spikes. Three-dimensional averaging showed that the surface glycoprotein (gp120) 'head' of each subunit of the trimeric SIV spike contains a primary mass, with two secondary lobes. The transmembrane glycoprotein 'stalk' of each trimer is composed of three independent legs that project obliquely from the trimer head, tripod-like. Reconciling available atomic structures with the three-dimensional whole spike density map yields insights into the orientation of Env spike structural elements and possible structural bases of their functions. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 687.2 KB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 11 KB 11 KB | 表示 表示 | ![]() |
画像 | ![]() | 35.1 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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リンク
EMDBのページ | ![]() ![]() |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | 3D map of SIVmac239 viral membrane. It is acquired by subtracting the 3D averaged volume of "top/bottom view" spikes from averaged volume of the "side view" spikes (supplementary method of the reference) . Author's threshold 2.25. It should be loaded together with the associated SIVmac239 envelope spike map (SIVmac239_Env_spike.map, EMD-1246, author's threshold 2.65 ). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 5.56 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
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試料の構成要素
-全体 : Membrane of SIVmac239 virus with truncated cytoplasmic tail
全体 | 名称: Membrane of SIVmac239 virus with truncated cytoplasmic tail |
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要素 |
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-超分子 #1000: Membrane of SIVmac239 virus with truncated cytoplasmic tail
超分子 | 名称: Membrane of SIVmac239 virus with truncated cytoplasmic tail タイプ: sample / ID: 1000 詳細: The virus was AT-2 treated to eliminate the infectivity. Number unique components: 1 |
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-超分子 #1: Simian immunodeficiency virus
超分子 | 名称: Simian immunodeficiency virus / タイプ: virus / ID: 1 / Name.synonym: SIVmac239 membrane / NCBI-ID: 11723 / 生物種: Simian immunodeficiency virus / 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: SIVmac239 membrane |
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宿主 | 生物種: ![]() |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | サブトモグラム平均法 |
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試料調製
緩衝液 | 詳細: PBS |
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グリッド | 詳細: 200 mesh Quantifoil R2/1 copper grid |
凍結 | 凍結剤: ETHANE / 装置: HOMEMADE PLUNGER / 詳細: Vitrification instrument: Home made plunger |
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電子顕微鏡法
顕微鏡 | FEI/PHILIPS CM300FEG/ST |
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詳細 | Minimum tilt angle was -70 |
日付 | 2004年8月30日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: TVIPS TEMCAM-F224 (2k x 2k) 実像数: 80 / 平均電子線量: 60 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 43200 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 6.0 µm / 最小 デフォーカス(公称値): 4.0 µm |
試料ステージ | 試料ホルダー: Gatan 626 cryoholder / 試料ホルダーモデル: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: 70 ° / Tilt series - Axis1 - Max angle: 70 ° |
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画像解析
詳細 | The tomographic tilt angle increment was determined by cosine rule, i.e., ~2-3 degrees increment around low tilt angles and <1 degree increment in the high tilt angles. Average number of tilts used in the 3D reconstructions: 80. Average tomographic tilt angle increment: 2. |
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最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 32.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Protomo 詳細: The resolution of the final averaged map, determined by Fourier shell correlation (based on a cutoff value of 0.5)is 2.5 nm and, after low pass filtering to the estimated first node in the ...詳細: The resolution of the final averaged map, determined by Fourier shell correlation (based on a cutoff value of 0.5)is 2.5 nm and, after low pass filtering to the estimated first node in the contrast transfer function, 3.2 nm. |