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基本情報
登録情報 | データベース: PDB / ID: 4udf | |||||||||
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タイトル | STRUCTURAL BASIS OF HUMAN PARECHOVIRUS NEUTRALIZATION BY HUMAN MONOCLONAL ANTIBODIES | |||||||||
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![]() | VIRUS / HUMAN PARECHOVIRUS 1 / HUMAN MONOCLONAL ANTIBODY / HPEV1-AM28 FAB | |||||||||
機能・相同性 | ![]() host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell ...host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / 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 / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding 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: 20 Å | |||||||||
![]() | Shakeel, S. / Westerhuis, B.M. / Ora, A. / Koen, G. / Bakker, A.Q. / Claassen, Y. / Beaumont, T. / Wolthers, K.C. / Butcher, S.J. | |||||||||
![]() | ![]() タイトル: Structural Basis of Human Parechovirus Neutralization by Human Monoclonal Antibodies. 著者: Shabih Shakeel / Brenda M Westerhuis / Ari Ora / Gerrit Koen / Arjen Q Bakker / Yvonne Claassen / Koen Wagner / Tim Beaumont / Katja C Wolthers / Sarah J Butcher / ![]() ![]() 要旨: Since it was first recognized in 2004 that human parechoviruses (HPeV) are a significant cause of central nervous system and neonatal sepsis, their clinical importance, primarily in children, has ...Since it was first recognized in 2004 that human parechoviruses (HPeV) are a significant cause of central nervous system and neonatal sepsis, their clinical importance, primarily in children, has started to emerge. Intravenous immunoglobulin treatment is the only treatment available in such life-threatening cases and has given moderate success. Direct inhibition of parechovirus infection using monoclonal antibodies is a potential treatment. We have developed two neutralizing monoclonal antibodies against HPeV1 and HPeV2, namely, AM18 and AM28, which also cross-neutralize other viruses. Here, we present the mapping of their epitopes using peptide scanning, surface plasmon resonance, fluorescence-based thermal shift assays, electron cryomicroscopy, and image reconstruction. We determined by peptide scanning and surface plasmon resonance that AM18 recognizes a linear epitope motif including the arginine-glycine-aspartic acid on the C terminus of capsid protein VP1. This epitope is normally used by the virus to attach to host cell surface integrins during entry and is found in 3 other viruses that AM18 neutralizes. Therefore, AM18 is likely to cause virus neutralization by aggregation and by blocking integrin binding to the capsid. Further, we show by electron cryomicroscopy, three-dimensional reconstruction, and pseudoatomic model fitting that ordered RNA interacts with HPeV1 VP1 and VP3. AM28 recognizes quaternary epitopes on the capsid composed of VP0 and VP3 loops from neighboring pentamers, thereby increasing the RNA accessibility temperature for the virus-AM28 complex compared to the virus alone. Thus, inhibition of RNA uncoating probably contributes to neutralization by AM28. IMPORTANCE: Human parechoviruses can cause mild infections to severe diseases in young children, such as neonatal sepsis, encephalitis, and cardiomyopathy. Intravenous immunoglobulin treatment is the ...IMPORTANCE: Human parechoviruses can cause mild infections to severe diseases in young children, such as neonatal sepsis, encephalitis, and cardiomyopathy. Intravenous immunoglobulin treatment is the only treatment available in such life-threatening cases. In order to develop more targeted treatment, we have searched for human monoclonal antibodies that would neutralize human parechoviruses 1 and 2, associated with mild infections such as gastroenteritis and severe infections of the central nervous system, and thus allow safe treatment. In the current study, we show how two such promising antibodies interact with the virus, modeling the atomic interactions between the virus and the antibody to propose how neutralization occurs. Both antibodies can cause aggregation; in addition, one antibody interferes with the virus recognizing its target cell, while the other, recognizing only the whole virus, inhibits the genome uncoating and replication in the cell. | |||||||||
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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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-検証レポート
文書・要旨 | ![]() | 999.5 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 12.2 MB | 表示 | |
XML形式データ | ![]() | 2.1 MB | 表示 | |
CIF形式データ | ![]() | 2.7 MB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-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: 20555.203 Da / 分子数: 60 / 断片: UNP residues 360-542 / 由来タイプ: 天然 詳細: FAB FRAGMENTS OF HUMAN MONOCLONAL ANTIBODY, AM28 WERE ATTACHED TO THE VIRUS 由来: (天然) ![]() 株: Harris 参照: UniProt: Q66578, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase #2: タンパク質 | 分子量: 25594.449 Da / 分子数: 60 / 断片: UNP residues 61-289 / 由来タイプ: 天然 詳細: FAB FRAGMENTS OF HUMAN MONOCLONAL ANTIBODY, AM28 WERE ATTACHED TO THE VIRUS 由来: (天然) ![]() 株: Harris 参照: UniProt: Q66578, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase #3: 抗体 | 分子量: 12168.451 Da / 分子数: 60 / 由来タイプ: 天然 / 由来: (天然) ![]() #4: 抗体 | 分子量: 13032.227 Da / 分子数: 60 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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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: AM28 FAB FRAGMENT IN COMPLEX WITH HUMAN PARECHOVIRUS 1 タイプ: VIRUS |
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ウイルスについての詳細 | ホストのカテゴリ: VERTEBRATES / 単離: STRAIN / タイプ: VIRION |
天然宿主 | 生物種: Homo sapiens |
緩衝液 | 名称: 10mM TRIS HCl, 150 mM NaCl, 1mM MgCl2 (1X TNM Buffer) pH: 7.5 詳細: 10mM TRIS HCl, 150 mM NaCl, 1mM MgCl2 (1X TNM Buffer) |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: HOLEY CARBON |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE / 詳細: LIQUID ETHANE |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Tecnai F20 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F20 / 日付: 2013年2月1日 |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 69000 X / 最大 デフォーカス(公称値): 4060 nm / 最小 デフォーカス(公称値): 1650 nm / Cs: 2 mm |
撮影 | 電子線照射量: 20 e/Å2 / フィルム・検出器のモデル: GENERIC GATAN |
画像スキャン | デジタル画像の数: 65 |
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解析
EMソフトウェア | 名称: Auto3DEM / カテゴリ: 3次元再構成 |
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CTF補正 | 詳細: WHOLE MICROGRAPH |
対称性 | 点対称性: I (正20面体型対称) |
3次元再構成 | 手法: POLAR FOURIER TRANSFORM / 解像度: 20 Å / 粒子像の数: 270 / ピクセルサイズ(公称値): 2.17 Å 倍率補正: SYMMETRY RELATED VP0 HELICES FITTING IN EM DENSITY 詳細: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2761 対称性のタイプ: POINT |
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL / Target criteria: Cross-correlation coefficient 詳細: METHOD--MOLECULAR DYNAMIC SIMULATION AND NORMAL MODE ANALYSIS REFINEMENT PROTOCOL--HOMOLOGY MODEL |
精密化 | 最高解像度: 20 Å |