+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-5122 | |||||||||
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タイトル | RNA-releasing poliovirus intermediates | |||||||||
マップデータ | LATE early RNA-releasing 80S poliovirus | |||||||||
試料 |
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キーワード | Picornavirus / poliovirus / intermediate / RNA-release / 80S | |||||||||
機能・相同性 | 機能・相同性情報 : / caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host translation initiation / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity ...: / caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host translation initiation / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding 類似検索 - 分子機能 | |||||||||
生物種 | poliovirus 1 mahoney (ポリオウイルス) | |||||||||
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: 10.0 Å | |||||||||
データ登録者 | Levy HC / Bostina M / Filman DJ / Hogle JM | |||||||||
引用 | ジャーナル: J Virol / 年: 2010 タイトル: Catching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy. 著者: Hazel C Levy / Mihnea Bostina / David J Filman / James M Hogle / 要旨: Poliovirus infection requires that the particle undergo a series of conformational transitions that lead to cell entry and genome release. In an effort to understand the conformational changes ...Poliovirus infection requires that the particle undergo a series of conformational transitions that lead to cell entry and genome release. In an effort to understand the conformational changes associated with the release of the RNA genome, we have used cryo-electron microscopy to characterize the structure of the 80S "empty" particles of poliovirus that are thought to represent the final product of the cell entry pathway. Using two-dimensional classification methods, we show that preparations of 80S particles contain at least two structures, which might represent snapshots from a continuous series of conformers. Using three-dimensional reconstruction methods, we have solved the structure of two distinct forms at subnanometric resolution, and we have built and refined pseudoatomic models into the reconstructions. The reconstructions and the derived models demonstrate that the two structural forms are both slightly expanded, resulting in partial disruption of interprotomer interfaces near their particle 2-fold axes, which may represent the site where RNA is released. The models demonstrate that each of the two 80S structures has undergone a unique set of movements of the capsid proteins, associated with rearrangement of flexible loops and amino-terminal extensions that participate in contacts between protomers, between pentamers, and with the viral RNA. | |||||||||
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_5122.map.gz | 4.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-5122-v30.xml emd-5122.xml | 10.3 KB 10.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_5122_1.tif | 1.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-5122 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5122 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_5122_validation.pdf.gz | 330.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_5122_full_validation.pdf.gz | 329.9 KB | 表示 | |
XML形式データ | emd_5122_validation.xml.gz | 6.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5122 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5122 | 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_5122.map.gz / 形式: CCP4 / 大きさ: 30.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | LATE early RNA-releasing 80S poliovirus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.3223 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 : 80S poliovirus
全体 | 名称: 80S poliovirus |
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要素 |
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-超分子 #1000: 80S poliovirus
超分子 | 名称: 80S poliovirus / タイプ: sample / ID: 1000 / 詳細: native virus heat-treated at 56 degrees C / 集合状態: 60 promoters arranged as a icosahedron / Number unique components: 1 |
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分子量 | 実験値: 8.3 MDa / 理論値: 8.3 MDa / 手法: Sedimentation |
-超分子 #1: poliovirus 1 mahoney
超分子 | 名称: poliovirus 1 mahoney / タイプ: virus / ID: 1 / Name.synonym: poliovirus 1 mahoney / 詳細: native virus is converted by heat-treatment to 80S / 生物種: poliovirus 1 mahoney / データベース: NCBI / ウイルスタイプ: VIRION / ウイルス・単離状態: SEROTYPE / ウイルス・エンベロープ: No / ウイルス・中空状態: Yes / Syn species name: poliovirus 1 mahoney |
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宿主 | 生物種: Homo sapiens (ヒト) / 別称: VERTEBRATES |
分子量 | 実験値: 8.3 MDa / 理論値: 8.3 MDa |
ウイルス殻 | Shell ID: 1 / 名称: capsid / 直径: 290 Å / T番号(三角分割数): 1 |
-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 | 0.2 mg/mL |
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緩衝液 | pH: 7.4 / 詳細: 20mM Tris, 50mM NaCl, 2 mM CaCl2 |
染色 | タイプ: NEGATIVE / 詳細: not stained |
グリッド | 詳細: 200 mesh copper grids |
凍結 | 凍結剤: ETHANE / 装置: HOMEMADE PLUNGER / 詳細: Vitrification instrument: home made plunger / 手法: blot for 3 secs |
-電子顕微鏡法
顕微鏡 | FEI TECNAI F30 |
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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: ZEISS SCAI / デジタル化 - サンプリング間隔: 7 µm / 実像数: 138 / 平均電子線量: 15 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: OTHER / 撮影モード: OTHER / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 0.9 µm / 倍率(公称値): 59000 |
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 |
実験機器 | モデル: Tecnai F30 / 画像提供: FEI Company |
-画像解析
詳細 | 10,000 particle were partitioned into two distinct classes |
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CTF補正 | 詳細: each micrograph |
最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 10.0 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: PFT2, EM3DR2 |