+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6o06 | |||||||||||||||
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タイトル | Extracellular factors prime enterovirus particles for uncoating | |||||||||||||||
要素 |
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キーワード | VIRUS / expanded particle | |||||||||||||||
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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / nucleoside-triphosphate phosphatase / protein complex oligomerization ...caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / 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 / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding 類似検索 - 分子機能 | |||||||||||||||
生物種 | Echovirus E1 (ウイルス) | |||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å | |||||||||||||||
データ登録者 | Domanska, A. / Ruokolainen, V. / Pelliccia, M. / Laajala, M. / Butcher, S.J. / Marjomaki, V.S. | |||||||||||||||
資金援助 | フィンランド, 4件
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引用 | ジャーナル: J Virol / 年: 2019 タイトル: Extracellular Albumin and Endosomal Ions Prime Enterovirus Particles for Uncoating That Can Be Prevented by Fatty Acid Saturation. 著者: Visa Ruokolainen / Aušra Domanska / Mira Laajala / Maria Pelliccia / Sarah J Butcher / Varpu Marjomäki / 要旨: There is limited information about the molecular triggers leading to the uncoating of enteroviruses under physiological conditions. Using real-time spectroscopy and sucrose gradients with ...There is limited information about the molecular triggers leading to the uncoating of enteroviruses under physiological conditions. Using real-time spectroscopy and sucrose gradients with radioactively labeled virus, we show at 37°C, the formation of albumin-triggered, metastable uncoating intermediate of echovirus 1 without receptor engagement. This conversion was blocked by saturating the albumin with fatty acids. High potassium but low sodium and calcium concentrations, mimicking the endosomal environment, also induced the formation of a metastable uncoating intermediate of echovirus 1. Together, these factors boosted the formation of the uncoating intermediate, and the infectivity of this intermediate was retained, as judged by end-point titration. Cryo-electron microscopy reconstruction of the virions treated with albumin and high potassium, low sodium, and low calcium concentrations resulted in a 3.6-Å resolution model revealing a fenestrated capsid showing 4% expansion and loss of the pocket factor, similarly to altered (A) particles described for other enteroviruses. The dimer interface between VP2 molecules was opened, the VP1 N termini disordered and most likely externalized. The RNA was clearly visible, anchored to the capsid. The results presented here suggest that extracellular albumin, partially saturated with fatty acids, likely leads to the formation of the infectious uncoating intermediate prior to the engagement with the cellular receptor. In addition, changes in mono- and divalent cations, likely occurring in endosomes, promote capsid opening and genome release. There is limited information about the uncoating of enteroviruses under physiological conditions. Here, we focused on physiologically relevant factors that likely contribute to opening of echovirus 1 and other B-group enteroviruses. By combining biochemical and structural data, we show that, before entering cells, extracellular albumin is capable of priming the virus into a metastable yet infectious intermediate state. The ionic changes that are suggested to occur in endosomes can further contribute to uncoating and promote genome release, once the viral particle is endocytosed. Importantly, we provide a detailed high-resolution structure of a virion after treatment with albumin and a preset ion composition, showing pocket factor release, capsid expansion, and fenestration and the clearly visible genome still anchored to the capsid. This study provides valuable information about the physiological factors that contribute to the opening of B group enteroviruses. | |||||||||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6o06.cif.gz | 224.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6o06.ent.gz | 177.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6o06.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 6o06_validation.pdf.gz | 1.3 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6o06_full_validation.pdf.gz | 1.3 MB | 表示 | |
XML形式データ | 6o06_validation.xml.gz | 32.5 KB | 表示 | |
CIF形式データ | 6o06_validation.cif.gz | 46.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/o0/6o06 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/6o06 | HTTPS FTP |
-関連構造データ
関連構造データ | 0565MC 4903C 6rjfC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10284 (タイトル: Extracellular albumin and endosomal ions prime enterovirus particles for uncoating that can be prevented by fatty acid saturation Data size: 2.4 TB Data #1: Unaligned multi-frame micrographs of control Echovirus 1 [micrographs - multiframe] Data #2: Unaligned multi-frame micrographs of control Echovirus 1 [micrographs - multiframe] Data #3: Unaligned multi-frame micrographs of treated Echovirus 1 (expanded particle) [micrographs - multiframe]) |
-リンク
-集合体
登録構造単位 |
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対称性 | 点対称性: (シェーンフリース記号: I (正20面体型対称)) |
-要素
#1: タンパク質 | 分子量: 31604.373 Da / 分子数: 1 / 断片: UNP residues 570-850 / 由来タイプ: 天然 / 由来: (天然) Echovirus E1 (ウイルス) / 参照: UniProt: O91734 |
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#2: タンパク質 | 分子量: 28126.465 Da / 分子数: 1 / 断片: UNP residues 77-330 / 由来タイプ: 天然 / 由来: (天然) Echovirus E1 (ウイルス) / 参照: UniProt: O91734 |
#3: タンパク質 | 分子量: 26471.074 Da / 分子数: 1 / 断片: UNP residues 331-569 / 由来タイプ: 天然 / 由来: (天然) Echovirus E1 (ウイルス) / 参照: UniProt: O91734 |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Echovirus E1 / タイプ: VIRUS / 詳細: Echovirus 1 was purified from infected GMK cells / Entity ID: all / 由来: NATURAL |
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分子量 | 単位: MEGADALTONS / 実験値: NO |
由来(天然) | 生物種: Echovirus E1 (ウイルス) |
ウイルスについての詳細 | 中空か: NO / エンベロープを持つか: NO / 単離: OTHER / タイプ: VIRION |
天然宿主 | 生物種: Homo sapiens |
ウイルス殻 | 名称: icosahedral / 直径: 300 nm / 三角数 (T数): 1 |
緩衝液 | pH: 7.2 詳細: 29 mM sodium chloride, 28 mM potassium ion, 0.145 mM magnesium chloride, 8 mM phosphate dibasic, 2 mM phosphate monobasic, 0.0093% faf-BSA |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドのタイプ: Quantifoil R2/2 |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TALOS ARCTICA |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 平均露光時間: 47.8 sec. / 電子線照射量: 30 e/Å2 フィルム・検出器のモデル: FEI FALCON III (4k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: I (正20面体型対称) | ||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 14615 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL | ||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 4JGY Accession code: 4JGY / Source name: PDB / タイプ: experimental model |