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基本情報
登録情報 | データベース: PDB / ID: 6sk7 | ||||||
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タイトル | Cryo-EM structure of rhinovirus-A89 | ||||||
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![]() | VIRUS / RV-A89 / HRV-B5 / capsid protein | ||||||
機能・相同性 | ![]() : / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / : / 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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane ...: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / : / 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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / DNA replication / host cell cytoplasm / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | Human rhinovirus A serotype 89 | ||||||
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: 2.9 Å | ||||||
![]() | Wald, J. / Goessweiner-Mohr, N. / Blaas, D. / Pasin, M. | ||||||
![]() | ![]() タイトル: Cryo-EM structure of pleconaril-resistant rhinovirus-B5 complexed to the antiviral OBR-5-340 reveals unexpected binding site. 著者: Jiri Wald / Marion Pasin / Martina Richter / Christin Walther / Neann Mathai / Johannes Kirchmair / Vadim A Makarov / Nikolaus Goessweiner-Mohr / Thomas C Marlovits / Irene Zanella / Antonio ...著者: Jiri Wald / Marion Pasin / Martina Richter / Christin Walther / Neann Mathai / Johannes Kirchmair / Vadim A Makarov / Nikolaus Goessweiner-Mohr / Thomas C Marlovits / Irene Zanella / Antonio Real-Hohn / Nuria Verdaguer / Dieter Blaas / Michaela Schmidtke / ![]() ![]() ![]() ![]() ![]() 要旨: Viral inhibitors, such as pleconaril and vapendavir, target conserved regions in the capsids of rhinoviruses (RVs) and enteroviruses (EVs) by binding to a hydrophobic pocket in viral capsid protein 1 ...Viral inhibitors, such as pleconaril and vapendavir, target conserved regions in the capsids of rhinoviruses (RVs) and enteroviruses (EVs) by binding to a hydrophobic pocket in viral capsid protein 1 (VP1). In resistant RVs and EVs, bulky residues in this pocket prevent their binding. However, recently developed pyrazolopyrimidines inhibit pleconaril-resistant RVs and EVs, and computational modeling has suggested that they also bind to the hydrophobic pocket in VP1. We studied the mechanism of inhibition of pleconaril-resistant RVs using RV-B5 (1 of the 7 naturally pleconaril-resistant rhinoviruses) and OBR-5-340, a bioavailable pyrazolopyrimidine with proven in vivo activity, and determined the 3D-structure of the protein-ligand complex to 3.6 Å with cryoelectron microscopy. Our data indicate that, similar to other capsid binders, OBR-5-340 induces thermostability and inhibits viral adsorption and uncoating. However, we found that OBR-5-340 attaches closer to the entrance of the pocket than most other capsid binders, whose viral complexes have been studied so far, showing only marginal overlaps of the attachment sites. Comparing the experimentally determined 3D structure with the control, RV-B5 incubated with solvent only and determined to 3.2 Å, revealed no gross conformational changes upon OBR-5-340 binding. The pocket of the naturally OBR-5-340-resistant RV-A89 likewise incubated with OBR-5-340 and solved to 2.9 Å was empty. Pyrazolopyrimidines have a rigid molecular scaffold and may thus be less affected by a loss of entropy upon binding. They interact with less-conserved regions than known capsid binders. Overall, pyrazolopyrimidines could be more suitable for the development of new, broadly active inhibitors. | ||||||
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構造ビューア | 分子: ![]() ![]() |
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-検証レポート
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文書・詳細版 | ![]() | 1.5 MB | 表示 | |
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CIF形式データ | ![]() | 52.7 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
登録構造単位 | ![]()
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要素
#1: タンパク質 | 分子量: 33288.102 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Virus grown in human cell line 由来: (天然) ![]() 参照: UniProt: P07210, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
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#2: タンパク質 | 分子量: 29422.793 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Virus grown in human cell line 由来: (天然) ![]() 参照: UniProt: P07210, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#3: タンパク質 | 分子量: 26325.994 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Virus grown in human cell line 由来: (天然) ![]() 参照: UniProt: P07210, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#4: タンパク質 | 分子量: 7461.104 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Virus grown in human cell line 由来: (天然) ![]() 参照: UniProt: D3KZ50 |
-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: Rhinovirus A / タイプ: VIRUS / Entity ID: all / 由来: NATURAL | ||||||||||||
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分子量 | 実験値: NO | ||||||||||||
由来(天然) | 生物種: ![]() | ||||||||||||
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: SEROTYPE / タイプ: VIRION | ||||||||||||
天然宿主 | 生物種: Homo sapiens | ||||||||||||
ウイルス殻 | 名称: VP1-4 / 直径: 302 nm | ||||||||||||
緩衝液 | pH: 7.4 | ||||||||||||
緩衝液成分 |
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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 / グリッドのタイプ: Homemade | ||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 100 % |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Tecnai Polara / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI POLARA 300 |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / Cs: 2.7 mm |
撮影 | 平均露光時間: 5 sec. / 電子線照射量: 40 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 実像数: 5370 |
画像スキャン | 動画フレーム数/画像: 25 / 利用したフレーム数/画像: 1-25 |
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解析
EMソフトウェア |
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CTF補正 | タイプ: NONE | ||||||||||||||||||||
対称性 | 点対称性: C60 (60回回転対称) | ||||||||||||||||||||
3次元再構成 | 解像度: 2.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 107054 / 対称性のタイプ: POINT | ||||||||||||||||||||
原子モデル構築 | 空間: REAL 詳細: Rosetta: DiMaio, F. et al. Atomic-accuracy models from 4.5-A cryo-electron microscopy data with density-guided iterative local refinement. Nat. Meth (2015). doi:10.1038/nmeth.3286 | ||||||||||||||||||||
原子モデル構築 | PDB-ID: 1AYM Accession code: 1AYM / Source name: PDB / タイプ: experimental model |