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基本情報
登録情報 | データベース: PDB / ID: 5lvc | ||||||
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タイトル | Aichi virus 1: empty particle | ||||||
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![]() | VIRUS / picornavirus / picornaviridae / Aichi virus 1 / empty particle / kobuvirus / 50 genome / release / human / pathogen / RNA | ||||||
機能・相同性 | ![]() host cell Golgi membrane / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / RNA helicase / symbiont entry into host cell ...host cell Golgi membrane / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / RNA helicase / symbiont entry into host cell / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane 類似検索 - 分子機能 | ||||||
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 | ||||||
![]() | Sabin, C. / Fuzik, T. / Skubnik, K. / Palkova, L. / Lindberg, A.M. / Plevka, P. | ||||||
![]() | ![]() タイトル: Structure of Aichi Virus 1 and Its Empty Particle: Clues to Kobuvirus Genome Release Mechanism. 著者: Charles Sabin / Tibor Füzik / Karel Škubník / Lenka Pálková / A Michael Lindberg / Pavel Plevka / ![]() ![]() 要旨: (AiV-1) is a human pathogen from the genus of the family. Worldwide, 80 to 95% of adults have antibodies against the virus. AiV-1 infections are associated with nausea, gastroenteritis, and fever. ... (AiV-1) is a human pathogen from the genus of the family. Worldwide, 80 to 95% of adults have antibodies against the virus. AiV-1 infections are associated with nausea, gastroenteritis, and fever. Unlike most picornaviruses, kobuvirus capsids are composed of only three types of subunits: VP0, VP1, and VP3. We present here the structure of the AiV-1 virion determined to a resolution of 2.1 Å using X-ray crystallography. The surface loop puff of VP0 and knob of VP3 in AiV-1 are shorter than those in other picornaviruses. Instead, the 42-residue BC loop of VP0 forms the most prominent surface feature of the AiV-1 virion. We determined the structure of AiV-1 empty particle to a resolution of 4.2 Å using cryo-electron microscopy. The empty capsids are expanded relative to the native virus. The N-terminal arms of capsid proteins VP0, which mediate contacts between the pentamers of capsid protein protomers in the native AiV-1 virion, are disordered in the empty capsid. Nevertheless, the empty particles are stable, at least , and do not contain pores that might serve as channels for genome release. Therefore, extensive and probably reversible local reorganization of AiV-1 capsid is required for its genome release. Aichi virus 1 (AiV-1) is a human pathogen that can cause diarrhea, abdominal pain, nausea, vomiting, and fever. AiV-1 is identified in environmental screening studies with higher frequency and greater abundance than other human enteric viruses. Accordingly, 80 to 95% of adults worldwide have suffered from AiV-1 infections. We determined the structure of the AiV-1 virion. Based on the structure, we show that antiviral compounds that were developed against related enteroviruses are unlikely to be effective against AiV-1. The surface of the AiV-1 virion has a unique topology distinct from other related viruses from the family. We also determined that AiV-1 capsids form compact shells even after genome release. Therefore, AiV-1 genome release requires large localized and probably reversible reorganization of the capsid. | ||||||
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構造の表示
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 149.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 115 KB | 表示 | ![]() |
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-検証レポート
文書・要旨 | ![]() | 795.8 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 798.2 KB | 表示 | |
XML形式データ | ![]() | 30.6 KB | 表示 | |
CIF形式データ | ![]() | 45.4 KB | 表示 | |
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-関連構造データ
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リンク
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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)) |
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要素
#1: タンパク質 | 分子量: 27194.688 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
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#2: タンパク質 | 分子量: 38950.758 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
#3: タンパク質 | 分子量: 24082.244 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: VP3 / 由来: (天然) ![]() |
-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: Aichi / タイプ: VIRUS / Entity ID: all / 由来: NATURAL |
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由来(天然) | 生物種: ![]() |
ウイルスについての詳細 | 中空か: YES / 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 |
緩衝液 | pH: 7.5 |
試料 | 濃度: 3 mg/ml / 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
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: ![]() |
電子レンズ | モード: BRIGHT FIELD / Cs: 2.7 mm / C2レンズ絞り径: 100 µm |
撮影 | 電子線照射量: 20 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
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解析
CTF補正 | タイプ: PHASE FLIPPING ONLY |
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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: 11606 / 対称性のタイプ: POINT |