+
データを開く
-
基本情報
登録情報 | データベース: EMDB / ID: EMD-5465 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-electron microscopy reconstruction of the Enterovirus 71 A-particle | |||||||||
![]() | Reconstruction of the Enterovirus 71 A-particle, produced by heat treating mature capsids in isotonic solution. | |||||||||
![]() |
| |||||||||
![]() | Enterovirus 71 / EV71 / A-particle / 135S | |||||||||
機能・相同性 | ![]() symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / 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 / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / 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 / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.3 Å | |||||||||
![]() | Shingler KL / Yoder JL / Carnegie MS / Ashley RE / Makhov AM / Conway JF / Hafenstein S | |||||||||
![]() | ![]() タイトル: The enterovirus 71 A-particle forms a gateway to allow genome release: a cryoEM study of picornavirus uncoating. 著者: Kristin L Shingler / Jennifer L Yoder / Michael S Carnegie / Robert E Ashley / Alexander M Makhov / James F Conway / Susan Hafenstein / ![]() 要旨: Since its discovery in 1969, enterovirus 71 (EV71) has emerged as a serious worldwide health threat. This human pathogen of the picornavirus family causes hand, foot, and mouth disease, and also has ...Since its discovery in 1969, enterovirus 71 (EV71) has emerged as a serious worldwide health threat. This human pathogen of the picornavirus family causes hand, foot, and mouth disease, and also has the capacity to invade the central nervous system to cause severe disease and death. Upon binding to a host receptor on the cell surface, the virus begins a two-step uncoating process, first forming an expanded, altered "A-particle", which is primed for genome release. In a second step after endocytosis, an unknown trigger leads to RNA expulsion, generating an intact, empty capsid. Cryo-electron microscopy reconstructions of these two capsid states provide insight into the mechanics of genome release. The EV71 A-particle capsid interacts with the genome near the icosahedral two-fold axis of symmetry, which opens to the external environment via a channel ∼10 Å in diameter that is lined with patches of negatively charged residues. After the EV71 genome has been released, the two-fold channel shrinks, though the overall capsid dimensions are conserved. These structural characteristics identify the two-fold channel as the site where a gateway forms and regulates the process of genome release. | |||||||||
履歴 |
|
-
構造の表示
ムービー |
![]() |
---|---|
構造ビューア | EMマップ: ![]() ![]() ![]() |
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 | ![]() | 65.4 MB | ![]() | |
---|---|---|---|---|
ヘッダ (付随情報) | ![]() ![]() | 12 KB 12 KB | 表示 表示 | ![]() |
画像 | ![]() | 978.2 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
EMDBのページ | ![]() ![]() |
---|---|
「今月の分子」の関連する項目 |
-
マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Reconstruction of the Enterovirus 71 A-particle, produced by heat treating mature capsids in isotonic solution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-
試料の構成要素
-全体 : Enterovirus 71 A-Particle
全体 | 名称: Enterovirus 71 A-Particle |
---|---|
要素 |
|
-超分子 #1000: Enterovirus 71 A-Particle
超分子 | 名称: Enterovirus 71 A-Particle / タイプ: sample / ID: 1000 詳細: The sample was purified mature virus heated in solution. 集合状態: icosahedral virus / Number unique components: 1 |
---|---|
分子量 | 実験値: 7 MDa / 理論値: 7 MDa / 手法: Calculation |
-超分子 #1: Human enterovirus 71
超分子 | 名称: Human enterovirus 71 / タイプ: virus / ID: 1 / Name.synonym: EV71, Hand foot and mouth disease virus / 詳細: purified virus in solution / NCBI-ID: 39054 / 生物種: Human enterovirus 71 / 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: No / Syn species name: EV71, Hand foot and mouth disease virus |
---|---|
宿主 | 生物種: ![]() |
分子量 | 実験値: 7 MDa / 理論値: 7 MDa |
ウイルス殻 | Shell ID: 1 / 名称: single capsid shell / 直径: 300 Å / T番号(三角分割数): 1 |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
![]() | 単粒子再構成法 |
試料の集合状態 | particle |
-
試料調製
濃度 | 0.1 mg/mL |
---|---|
緩衝液 | pH: 7.5 / 詳細: 10 mM Tris-HCl, 20 mM NaCl, 5 mM MgCl2 |
グリッド | 詳細: glow discharged holey carbon Quantifoil electron microscopy grids |
凍結 | 凍結剤: ETHANE-PROPANE MIXTURE / チャンバー内湿度: 95 % / チャンバー内温度: 76 K / 装置: FEI VITROBOT MARK III |
-
電子顕微鏡法
顕微鏡 | FEI TECNAI F20 |
---|---|
温度 | 平均: 95 K |
アライメント法 | Legacy - 非点収差: CTFFIND3 (EMAN) |
日付 | 2012年4月17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: 6.35 µm / 実像数: 40 / 平均電子線量: 15 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 50000 / 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD / Cs: 2 mm / 最大 デフォーカス(公称値): 4.28 µm / 最小 デフォーカス(公称値): 1.73 µm / 倍率(公称値): 50000 |
試料ステージ | 試料ホルダーモデル: GATAN LIQUID NITROGEN |
実験機器 | ![]() モデル: Tecnai F20 / 画像提供: FEI Company |
-
画像解析
詳細 | The particles were selected using an automatic selection program (EMAN). |
---|---|
CTF補正 | 詳細: auto3DEM |
最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 6.3 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: EMAN2, auto3DEM / 詳細: A single data set was used for the reconstruction / 使用した粒子像数: 11436 |
-原子モデル構築 1
初期モデル | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C |
---|---|
ソフトウェア | 名称: Chimera, Situs |
詳細 | Protocol: rigid body. One protomer was fit in Chimera, used to generate a full crystal map, then docked as a rigid body using Situs into the cryoEM density map. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: correlation coefficient |
得られたモデル | ![]() PDB-3j22: |