+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7n6y | ||||||
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タイトル | Mouse norovirus (MNV-1) capsid at pH 5.0 | ||||||
要素 | Capsid protein | ||||||
キーワード | VIRUS / norovirus / mouse / pH 5.0 | ||||||
機能・相同性 | Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virion component / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / Capsid protein VP1 機能・相同性情報 | ||||||
生物種 | Murine norovirus 1 (マウスノロウイルス 1) | ||||||
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: 3.3 Å | ||||||
データ登録者 | Smith, T.J. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: J Virol / 年: 2021 タイトル: Multiple Signals in the Gut Contract the Mouse Norovirus Capsid To Block Antibody Binding While Enhancing Receptor Affinity. 著者: Alexis N Williams / Michael B Sherman / Hong Q Smith / Stefan Taube / B Montgomery Pettitt / Christiane E Wobus / Thomas J Smith / 要旨: Human norovirus is the leading cause of gastroenteritis worldwide, with no approved vaccine or antiviral treatment to mitigate infection. These plus-strand RNA viruses have T = 3 icosahedral ...Human norovirus is the leading cause of gastroenteritis worldwide, with no approved vaccine or antiviral treatment to mitigate infection. These plus-strand RNA viruses have T = 3 icosahedral protein capsids with 90 pronounced protruding (P) domain dimers, to which antibodies and cellular receptors bind. We previously demonstrated that bile binding to the capsid of mouse norovirus (MNV) causes several major conformational changes; the entire P domain rotates by ∼90° and contracts onto the shell, the P domain dimers rotate about each other, and the structural equilibrium of the epitopes at the top of the P domain shifts toward the closed conformation, which favors receptor binding while blocking antibody binding. Here, we demonstrate that MNV undergoes reversible conformational changes at pH 5.0 that are nearly identical to those observed when bile binds. Notably, at low pH or when metals bind, a cluster of acidic resides in the G'-H' loop interact and distort the G'-H' loop, and this may drive C'-D' loop movement toward the closed conformation. Enzyme-linked immunosorbent assays with infectious virus particles at low pH or in the presence of metals demonstrated that all tested antibodies do not bind to this contracted form, akin to what was observed with the MNV-bile complex. Therefore, low pH, cationic metals, and bile salts are physiological triggers in the gut for P domain contraction and structural rearrangement, which synergistically prime the virus for receptor binding while blocking antibody binding. The protruding domains on the calicivirus capsids are recognized by cell receptors and antibodies. We demonstrated that MNV P domains are highly mobile, and bile causes contraction onto the shell surface while allosterically blocking antibody binding. We present the near-atomic cryo-electron microscopy structures of infectious MNV at pH 5.0 and pH 7.5. Surprisingly, low pH is sufficient to cause the same conformational changes as when bile binds. A cluster of acidic residues on the G'-H' loop were most likely involved in the pH effects. These residues also bound divalent cations and had the same conformation as observed here at pH 5. Binding assays demonstrated that low pH and metals block antibody binding, and thus the G'-H' loop might be driving the conformational changes. Therefore, low pH, cationic metals, and bile salts in the gut synergistically prime the virus for receptor binding while blocking antibody binding. | ||||||
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 | 7n6y.cif.gz | 263.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7n6y.ent.gz | 215.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7n6y.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 | 7n6y_validation.pdf.gz | 973 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7n6y_full_validation.pdf.gz | 994 KB | 表示 | |
XML形式データ | 7n6y_validation.xml.gz | 48.7 KB | 表示 | |
CIF形式データ | 7n6y_validation.cif.gz | 72.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/n6/7n6y ftp://data.pdbj.org/pub/pdb/validation_reports/n6/7n6y | HTTPS FTP |
-関連構造データ
-リンク
-集合体
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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: 58700.660 Da / 分子数: 3 / 由来タイプ: 天然 由来: (天然) Murine norovirus 1 (マウスノロウイルス 1) 参照: UniProt: Q80J94 |
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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 |
-試料調製
構成要素 | 名称: Murine norovirus 1 / タイプ: VIRUS / Entity ID: all / 由来: NATURAL |
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由来(天然) | 生物種: Murine norovirus 1 (マウスノロウイルス 1) |
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: STRAIN / タイプ: VIRION |
天然宿主 | 生物種: Mus musculus |
ウイルス殻 | 三角数 (T数): 3 |
緩衝液 | pH: 5 / 詳細: 25mM Citrate, 25mM phosphate, 100mM NaCl, pH 5.0 |
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-PROPANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 48 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.15_3448: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 14244 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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