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基本情報
登録情報 | データベース: PDB / ID: 8yf8 | |||||||||
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タイトル | Cryo-EM structure of Dragon Grouper nervous necrosis virus-like particle at pH5.0 (3.52A) | |||||||||
![]() | Capsid protein alpha | |||||||||
![]() | VIRUS / nervous necrosis virus / Dragon Grouper / Cryo-EM structure | |||||||||
機能・相同性 | Nodavirus capsid / nodavirus capsid protein / Viral coat protein subunit / viral capsid / Capsid protein alpha![]() | |||||||||
生物種 | ![]() | |||||||||
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: 3.52 Å | |||||||||
![]() | Wang, C.H. / Chang, W.H. | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Molecular Mechanism of pH-Induced Protrusion Configuration Switching in Piscine Betanodavirus Implies a Novel Antiviral Strategy. 著者: Petra Štěrbová / Chun-Hsiung Wang / Kathleen J D Carillo / Yuan-Chao Lou / Takayuki Kato / Keiichi Namba / Der-Lii M Tzou / Wei-Hau Chang / ![]() ![]() 要旨: Many viruses contain surface spikes or protrusions that are essential for virus entry. These surface structures can thereby be targeted by antiviral drugs to treat viral infections. Nervous necrosis ...Many viruses contain surface spikes or protrusions that are essential for virus entry. These surface structures can thereby be targeted by antiviral drugs to treat viral infections. Nervous necrosis virus (NNV), a simple nonenveloped virus in the genus of betanodavirus, infects fish and damages aquaculture worldwide. NNV has 60 conspicuous surface protrusions, each comprising three protrusion domains (P-domain) of its capsid protein. NNV uses protrusions to bind to common receptors of sialic acids on the host cell surface to initiate its entry via the endocytic pathway. However, structural alterations of NNV in response to acidic conditions encountered during this pathway remain unknown, while detailed interactions of protrusions with receptors are unclear. Here, we used cryo-EM to discover that Grouper NNV protrusions undergo low-pH-induced compaction and resting. NMR and molecular dynamics (MD) simulations were employed to probe the atomic details. A solution structure of the P-domain at pH 7.0 revealed a long flexible loop (amino acids 311-330) and a pocket outlined by this loop. Molecular docking analysis showed that the N-terminal moiety of sialic acid inserted into this pocket to interact with conserved residues inside. MD simulations demonstrated that part of this loop converted to a β-strand under acidic conditions, allowing for P-domain trimerization and compaction. Additionally, a low-pH-favored conformation is attained for the linker connecting the P-domain to the NNV shell, conferring resting protrusions. Our findings uncover novel pH-dependent conformational switching mechanisms underlying NNV protrusion dynamics potentially utilized for facilitating NNV entry, providing new structural insights into complex NNV-host interactions with the identification of putative druggable hotspots on the protrusion. | |||||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
関連構造データ | ![]() 39214 ![]() 39212 ![]() 39213 ![]() 39215 ![]() 39217 ![]() 8yf6C ![]() 8yf7C ![]() 8yf9C 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 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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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)) |
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要素
#1: タンパク質 | 分子量: 37128.754 Da / 分子数: 3 / 由来タイプ: 組換発現 由来: (組換発現) ![]() 発現宿主: ![]() ![]() #2: 化合物 | 研究の焦点であるリガンドがあるか | Y | |
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-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 |
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試料調製
構成要素 | 名称: Dragon Grouper nervous necrosis virus-like particle at pH5.0 (180 subunits) タイプ: COMPLEX / Entity ID: #1 / 由来: RECOMBINANT |
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由来(天然) | 生物種: ![]() |
由来(組換発現) | 生物種: ![]() ![]() |
緩衝液 | pH: 5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
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電子顕微鏡撮影
顕微鏡 | モデル: JEOL 2100F |
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電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2930 nm / 最小 デフォーカス(公称値): 870 nm |
撮影 | 電子線照射量: 30 e/Å2 フィルム・検出器のモデル: DIRECT ELECTRON DE-20 (5k x 3k) |
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解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3次元再構成 | 解像度: 3.52 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 22364 / 対称性のタイプ: POINT |