+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-5726 | |||||||||
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タイトル | Three-dimensional Structure of Victorivirus HvV190S | |||||||||
マップデータ | Reconstruction of HvV190S Virus Like Particle lacking the dsRNA genome | |||||||||
試料 |
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生物種 | Helminthosporium victoriae virus 190S (ウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / ネガティブ染色法 / 解像度: 7.5 Å | |||||||||
データ登録者 | Dun SE / Li H / Cardone G / Nibert ML / Gabrial SA / Baker TS | |||||||||
引用 | ジャーナル: PLoS Pathog / 年: 2013 タイトル: Three-dimensional structure of victorivirus HvV190S suggests coat proteins in most totiviruses share a conserved core. 著者: Sarah E Dunn / Hua Li / Giovanni Cardone / Max L Nibert / Said A Ghabrial / Timothy S Baker / 要旨: Double-stranded (ds)RNA fungal viruses are currently assigned to six different families. Those from the family Totiviridae are characterized by nonsegmented genomes and single-layer capsids, 300-450 ...Double-stranded (ds)RNA fungal viruses are currently assigned to six different families. Those from the family Totiviridae are characterized by nonsegmented genomes and single-layer capsids, 300-450 Å in diameter. Helminthosporium victoriae virus 190S (HvV190S), prototype of recently recognized genus Victorivirus, infects the filamentous fungus Helminthosporium victoriae (telomorph: Cochliobolus victoriae), which is the causal agent of Victoria blight of oats. The HvV190S genome is 5179 bp long and encompasses two large, slightly overlapping open reading frames that encode the coat protein (CP, 772 aa) and the RNA-dependent RNA polymerase (RdRp, 835 aa). To our present knowledge, victoriviruses uniquely express their RdRps via a coupled termination-reinitiation mechanism that differs from the well-characterized Saccharomyces cerevisiae virus L-A (ScV-L-A, prototype of genus Totivirus), in which the RdRp is expressed as a CP/RdRp fusion protein due to ribosomal frameshifting. Here, we used transmission electron cryomicroscopy and three-dimensional image reconstruction to determine the structures of HvV190S virions and two types of virus-like particles (capsids lacking dsRNA and capsids lacking both dsRNA and RdRp) at estimated resolutions of 7.1, 7.5, and 7.6 Å, respectively. The HvV190S capsid is thin and smooth, and contains 120 copies of CP arranged in a "T = 2" icosahedral lattice characteristic of ScV-L-A and other dsRNA viruses. For aid in our interpretations, we developed and used an iterative segmentation procedure to define the boundaries of the two, chemically identical CP subunits in each asymmetric unit. Both subunits have a similar fold, but one that differs from ScV-L-A in many details except for a core α-helical region that is further predicted to be conserved among many other totiviruses. In particular, we predict the structures of other victoriviruses to be highly similar to HvV190S and the structures of most if not all totiviruses including, Leishmania RNA virus 1, to be similar as well. | |||||||||
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_5726.map.gz | 26.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-5726-v30.xml emd-5726.xml | 10.9 KB 10.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_5726_1.jpg | 292.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-5726 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5726 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_5726_validation.pdf.gz | 78.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_5726_full_validation.pdf.gz | 77.6 KB | 表示 | |
XML形式データ | emd_5726_validation.xml.gz | 494 B | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5726 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5726 | 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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-マップ
ファイル | ダウンロード / ファイル: emd_5726.map.gz / 形式: CCP4 / 大きさ: 234.2 MB / タイプ: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of HvV190S Virus Like Particle lacking the dsRNA genome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.07 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 : Helminthosporium victoriae virus 190S VLP-C+
全体 | 名称: Helminthosporium victoriae virus 190S VLP-C+ |
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要素 |
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-超分子 #1000: Helminthosporium victoriae virus 190S VLP-C+
超分子 | 名称: Helminthosporium victoriae virus 190S VLP-C+ / タイプ: sample / ID: 1000 / 集合状態: Icosahedral / Number unique components: 1 |
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-超分子 #1: Helminthosporium victoriae virus 190S
超分子 | 名称: Helminthosporium victoriae virus 190S / タイプ: virus / ID: 1 / Name.synonym: HvV190S-VLP-C+ / NCBI-ID: 45237 / 生物種: Helminthosporium victoriae virus 190S / Sci species strain: B-2 / ウイルスタイプ: VIRUS-LIKE PARTICLE / ウイルス・単離状態: STRAIN / ウイルス・エンベロープ: No / ウイルス・中空状態: Yes / Syn species name: HvV190S-VLP-C+ |
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宿主 | 生物種: Cochliobolus victoriae (菌類) / 別称: FUNGI |
Host system | 生物種: unidentified (未定義) |
ウイルス殻 | Shell ID: 1 / 直径: 462 Å / T番号(三角分割数): 2 |
-実験情報
-構造解析
手法 | ネガティブ染色法, クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 5 mg/mL |
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緩衝液 | pH: 7.8 / 詳細: 50 mM Tris-HCl, 5 mM EDTA, 150 mM NaCl, pH 7.8 |
染色 | タイプ: NEGATIVE 詳細: Samples were adsorbed to continuous carbon grids that had been glow-discharged for ~25 seconds in an Emitech K350 evaporation unit. Samples were subsequently stained with 1% aqueous uranyl ...詳細: Samples were adsorbed to continuous carbon grids that had been glow-discharged for ~25 seconds in an Emitech K350 evaporation unit. Samples were subsequently stained with 1% aqueous uranyl acetate and rinsed with ddH2O. |
グリッド | 詳細: 200 mesh carbon grid with thin carbon support. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 90 K / 装置: FEI VITROBOT MARK III 詳細: Vitrification carried out after applying sample to carbon-coated grids and waiting 5 minutes before inserting the grid into the Vitrobot. 手法: Blot for 3.5 seconds before plunging. |
-電子顕微鏡法
顕微鏡 | FEI POLARA 300 |
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温度 | 最低: 90 K / 最高: 92 K / 平均: 91 K |
アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected at 120,000 times magnification using FFT |
日付 | 2009年8月8日 |
撮影 | カテゴリ: FILM / フィルム・検出器のモデル: KODAK SO-163 FILM デジタル化 - スキャナー: NIKON SUPER COOLSCAN 9000 デジタル化 - サンプリング間隔: 1.07 µm / 実像数: 289 / 平均電子線量: 24 e/Å2 / ビット/ピクセル: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
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: 2.3 mm / 最大 デフォーカス(公称値): 3.89 µm / 最小 デフォーカス(公称値): 0.69 µm / 倍率(公称値): 59000 |
試料ステージ | 試料ホルダーモデル: OTHER |
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
-画像解析
CTF補正 | 詳細: ROBEM |
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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: 7.5 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: AUTO3DEM / 使用した粒子像数: 16046 |