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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 9opc | |||||||||||||||||||||||||||
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タイトル | Herpes simplex virus type 1 (HSV-1) C-capsid pUL6 portal protein, dodecameric complex | |||||||||||||||||||||||||||
![]() | Capsid portal protein | |||||||||||||||||||||||||||
![]() | VIRAL PROTEIN / Complex | |||||||||||||||||||||||||||
機能・相同性 | Herpesvirus portal protein / Herpesvirus UL6 like / chromosome organization / virion component / host cell nucleus / Capsid portal protein![]() | |||||||||||||||||||||||||||
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: 4.2 Å | |||||||||||||||||||||||||||
![]() | Crofut, E.H. / Kashyap, S. / Stevens, A. / Jih, J. / Liu, Y.-T. / Zhou, Z.H. | |||||||||||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure of a new capsid form and comparison with A-, B-, and C-capsids clarify herpesvirus assembly. 著者: Alexander Stevens / Saarang Kashyap / Ethan Crofut / Ana Lucia Alvarez-Cabrera / Jonathan Jih / Yun-Tao Liu / Z Hong Zhou / ![]() 要旨: Three capsid types have been recognized from the nuclei of herpesvirus-infected cells: empty A-capsids, scaffolding-containing B-capsids, and DNA-filled C-capsids. Despite progress in determining ...Three capsid types have been recognized from the nuclei of herpesvirus-infected cells: empty A-capsids, scaffolding-containing B-capsids, and DNA-filled C-capsids. Despite progress in determining atomic structures of these capsids and extracellular virions in recent years, debate persists concerning the origins and temporal relationships among these capsids during capsid assembly and genome packaging. Here, we have imaged over 300,000 capsids of herpes simplex virus type 1 by cryogenic electron microscopy (cryoEM) and exhaustively classified them to characterize the structural heterogeneity of the DNA-translocating portal complex and their functional states. The resultant atomic structures reveal not only the expected A-, B-, and C-capsids but also capsids with portal vertices similar to C-capsids but no resolvable genome in the capsid lumen, which we named D-capsids. The dodecameric dsDNA-translocating portal complex varies across these capsid types in their radial positions in icosahedral capsids and exhibits structural dynamics within each capsid type. In D-capsids, terminal DNA density exists in multiple conformations including one reminiscent of that in C-capsids, suggesting D-capsids are products of failed DNA retention. This interpretation is supported by varying amounts of DNA outside individual D-capsids and by the correlation of capsid counts observed of infected cell nuclei and those after purification. Additionally, an "anchoring" segment of the scaffold protein is resolved interacting with the portal baskets of A- and B-capsids but not D- and C-capsids. Taken together, our data indicate that A-capsids arise from failed DNA packaging and D-capsids from failed genome retention, clarifying the origins of empty capsids in herpesvirus assembly.IMPORTANCEAs the prototypical herpesvirus, herpes simplex virus 1 (HSV-1) exhibits a global seroprevalence of 67% and approaching 90% in some localities. Herpesvirus infections can cause devastating cancers and birth defects, with HSV-1 infections leading to cold sores among the general population worldwide and blindness in developing nations. Here, we present atomic structures of the capsids sorted out from the nuclear isolates of HSV-1 infected cells, including the previously recognized A-, B-, and C-capsids, as well as the newly identified D-capsid. The structures show the details of protein-protein and protein-DNA interactions within each capsid type and the positional and interactional variability of the viral DNA-translocating portal vertex among these capsids. Importantly, our findings suggest that A-capsids are products of failed dsDNA packaging and D-capsids of failed genome retention. Together, the high-resolution 3D structures clarify the processes of genome packaging, maintenance, and ejection during capsid assembly, which are conserved across all herpesviruses. | |||||||||||||||||||||||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 875.8 KB | 表示 | ![]() |
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PDB形式 | ![]() | 724.8 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.7 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.7 MB | 表示 | |
XML形式データ | ![]() | 135.1 KB | 表示 | |
CIF形式データ | ![]() | 206.5 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 70691MC ![]() 9op4C ![]() 9op5C ![]() 9op8C ![]() 9opbC ![]() 9opvC 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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要素
#1: タンパク質 | 分子量: 74178.523 Da / 分子数: 12 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 参照: UniProt: H9E912 Has protein modification | N | |
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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: Dodecameric complex of pUL6 / タイプ: COMPLEX / Entity ID: all / 由来: NATURAL |
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分子量 | 実験値: NO |
由来(天然) | 生物種: ![]() ![]() |
緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil |
急速凍結 | 凍結剤: ETHANE |
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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: TFS KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 81000 X / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 1500 nm / Cs: 2.7 mm |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 電子線照射量: 45 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
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解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 232140 / 対称性のタイプ: POINT |