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基本情報
登録情報 | データベース: EMDB / ID: EMD-1514 | |||||||||
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タイトル | Cryoelectron tomography of HIV-1 envelope spikes | |||||||||
![]() | Raw tomogram of HIV-1 BaL virus. No filter applied. | |||||||||
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![]() | HIV-1 / envelope spikes / cryo electron tomography | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 電子線トモグラフィー法 / クライオ電子顕微鏡法 | |||||||||
![]() | Zhu P / Winkler H / Chertova E / Taylor KA / Roux KH | |||||||||
![]() | ![]() タイトル: Cryoelectron tomography of HIV-1 envelope spikes: further evidence for tripod-like legs. 著者: Ping Zhu / Hanspeter Winkler / Elena Chertova / Kenneth A Taylor / Kenneth H Roux / ![]() 要旨: A detailed understanding of the morphology of the HIV-1 envelope (Env) spike is key to understanding viral pathogenesis and for informed vaccine design. We have previously presented a cryoelectron ...A detailed understanding of the morphology of the HIV-1 envelope (Env) spike is key to understanding viral pathogenesis and for informed vaccine design. We have previously presented a cryoelectron microscopic tomogram (cryoET) of the Env spikes on SIV virions. Several structural features were noted in the gp120 head and gp41 stalk regions. Perhaps most notable was the presence of three splayed legs projecting obliquely from the base of the spike head toward the viral membrane. Subsequently, a second 3D image of SIV spikes, also obtained by cryoET, was published by another group which featured a compact vertical stalk. We now report the cryoET analysis of HIV-1 virion-associated Env spikes using enhanced analytical cryoET procedures. More than 2,000 Env spike volumes were initially selected, aligned, and sorted into structural classes using algorithms that compensate for the "missing wedge" and do not impose any symmetry. The results show varying morphologies between structural classes: some classes showed trimers in the head domains; nearly all showed two or three legs, though unambiguous three-fold symmetry was not observed either in the heads or the legs. Subsequently, clearer evidence of trimeric head domains and three splayed legs emerged when head and leg volumes were independently aligned and classified. These data show that HIV-1, like SIV, also displays the tripod-like leg configuration, and, unexpectedly, shows considerable gp41 leg flexibility/heteromorphology. The tripod-like model for gp41 is consistent with, and helps explain, many of the unique biophysical and immunological features of this region. | |||||||||
履歴 |
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構造の表示
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添付画像 |
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マップデータ | ![]() | 203.8 KB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 9.1 KB 9.1 KB | 表示 表示 | ![]() |
画像 | ![]() | 125 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Raw tomogram of HIV-1 BaL virus. No filter applied. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : HIV-1 BaL / SUPT1-CCR5 CL.30, provided by the AIDS Vaccine Progra...
全体 | 名称: HIV-1 BaL / SUPT1-CCR5 CL.30, provided by the AIDS Vaccine Program, SAIC Frederick, Inc., NCI, Frederick, MD. Lot p3955. |
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要素 |
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-超分子 #1000: HIV-1 BaL / SUPT1-CCR5 CL.30, provided by the AIDS Vaccine Progra...
超分子 | 名称: HIV-1 BaL / SUPT1-CCR5 CL.30, provided by the AIDS Vaccine Program, SAIC Frederick, Inc., NCI, Frederick, MD. Lot p3955. タイプ: sample / ID: 1000 詳細: The map is the raw tomogram of HIV-1 BaL virus. The envelope spikes (trimer of gp120 and ecto domain of gp41, total MW is about 0.45 MegaDaltons)on the virion surface were picked up and ...詳細: The map is the raw tomogram of HIV-1 BaL virus. The envelope spikes (trimer of gp120 and ecto domain of gp41, total MW is about 0.45 MegaDaltons)on the virion surface were picked up and subject to 3D alignment and classification analysis. 集合状態: Highly purified virus. The envelope spikes on the virion surface are trimer. Number unique components: 1 |
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-超分子 #1: Human immunodeficiency virus 1
超分子 | 名称: Human immunodeficiency virus 1 / タイプ: virus / ID: 1 詳細: The envelope spikes are distributed on the surface of HIV-1 virions. NCBI-ID: 11676 / 生物種: Human immunodeficiency virus 1 / 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 |
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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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![]() | 電子線トモグラフィー法 |
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試料調製
濃度 | 2.8 mg/mL |
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緩衝液 | pH: 7.4 / 詳細: Originally in TNE, resuspend in PBS |
グリッド | 詳細: 300 mesh R2/1 Quantifoil grid |
凍結 | 凍結剤: ETHANE / 装置: HOMEMADE PLUNGER 詳細: Vitrification instrument: Home made. Vitrification carried out in cold room 手法: Blot for 5-6 seconds before plunging |
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電子顕微鏡法
顕微鏡 | FEI/PHILIPS CM300FEG/T |
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温度 | 平均: 97 K |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: TVIPS TEMCAM-F224 (2k x 2k) 平均電子線量: 1.5 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2 mm / 最大 デフォーカス(公称値): 4.0 µm / 倍率(公称値): 43200 |
試料ステージ | 試料ホルダー: Eucentric / 試料ホルダーモデル: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -69 ° / Tilt series - Axis1 - Max angle: 64 ° / Tilt series - Axis1 - Angle increment: 2 ° |
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画像解析
詳細 | The tilt angles were determined using saxton schedule. The angle increment is 2 deg at low tilt angles range and decreased to about 1 deg at high tilt angles range. |
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最終 再構成 | アルゴリズム: OTHER / ソフトウェア - 名称: PROTOMO / 使用した粒子像数: 86 |