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基本情報
登録情報 | データベース: EMDB / ID: EMD-6383 | |||||||||
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タイトル | The cryoEM map of EV71 empty particle in complex with the Fab fragment of antibody D5 | |||||||||
![]() | The cryoEM map of EV71 empty particle in complex with the Fab fragment of antibody D5 | |||||||||
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![]() | Enterovirus 71(EV71) / virus-antibody complex / bivalent binding / high resolution cryo-EM | |||||||||
機能・相同性 | ![]() RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / viral capsid / symbiont-mediated suppression of host gene expression / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / 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 / nucleus / metal ion binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / ネガティブ染色法 / 解像度: 6.0 Å | |||||||||
![]() | Fan C / Ye XH / Ku ZQ / Zuo T / Kong LL / Zhang C / Shi JP / Liu QW / Chen T / Zhang YY ...Fan C / Ye XH / Ku ZQ / Zuo T / Kong LL / Zhang C / Shi JP / Liu QW / Chen T / Zhang YY / Jiang W / Zhang LQ / Huang Z / Cong Y | |||||||||
![]() | ![]() タイトル: Structural Basis for Recognition of Human Enterovirus 71 by a Bivalent Broadly Neutralizing Monoclonal Antibody. 著者: Xiaohua Ye / Chen Fan / Zhiqiang Ku / Teng Zuo / Liangliang Kong / Chao Zhang / Jinping Shi / Qingwei Liu / Tan Chen / Yingyi Zhang / Wen Jiang / Linqi Zhang / Zhong Huang / Yao Cong / ![]() ![]() 要旨: Enterovirus 71 (EV71) is the main pathogen responsible for hand, foot and mouth disease with severe neurological complications and even death in young children. We have recently identified a highly ...Enterovirus 71 (EV71) is the main pathogen responsible for hand, foot and mouth disease with severe neurological complications and even death in young children. We have recently identified a highly potent anti-EV71 neutralizing monoclonal antibody, termed D5. Here we investigated the structural basis for recognition of EV71 by the antibody D5. Four three-dimensional structures of EV71 particles in complex with IgG or Fab of D5 were reconstructed by cryo-electron microscopy (cryo-EM) single particle analysis all at subnanometer resolutions. The most critical EV71 mature virion-Fab structure was resolved to a resolution of 4.8 Å, which is rare in cryo-EM studies of virus-antibody complex so far. The structures reveal a bivalent binding pattern of D5 antibody across the icosahedral 2-fold axis on mature virion, suggesting that D5 binding may rigidify virions to prevent their conformational changes required for subsequent RNA release. Moreover, we also identified that the complementary determining region 3 (CDR3) of D5 heavy chain directly interacts with the extremely conserved VP1 GH-loop of EV71, which was validated by biochemical and virological assays. We further showed that D5 is indeed able to neutralize a variety of EV71 genotypes and strains. Moreover, D5 could potently confer protection in a mouse model of EV71 infection. Since the conserved VP1 GH-loop is involved in EV71 binding with its uncoating receptor, the scavenger receptor class B, member 2 (SCARB2), the broadly neutralizing ability of D5 might attribute to its inhibition of EV71 from binding SCARB2. Altogether, our results elucidate the structural basis for the binding and neutralization of EV71 by the broadly neutralizing antibody D5, thereby enhancing our understanding of antibody-based protection against EV71 infection. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 21.7 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 12.8 KB 12.8 KB | 表示 表示 | ![]() |
画像 | ![]() | 992 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | The cryoEM map of EV71 empty particle in complex with the Fab fragment of antibody D5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.79 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
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試料の構成要素
-全体 : EV71 empty particle in complex with the Fab fragment of antibody D5
全体 | 名称: EV71 empty particle in complex with the Fab fragment of antibody D5 |
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要素 |
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-超分子 #1000: EV71 empty particle in complex with the Fab fragment of antibody D5
超分子 | 名称: EV71 empty particle in complex with the Fab fragment of antibody D5 タイプ: sample / ID: 1000 集合状態: One fab fragment of antibody D5 bind to one protomer of EV71 Number unique components: 2 |
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分子量 | 理論値: 8 MDa |
-超分子 #1: Human enterovirus 71
超分子 | 名称: Human enterovirus 71 / タイプ: virus / ID: 1 / NCBI-ID: 39054 / 生物種: Human enterovirus 71 / Sci species strain: G082 / データベース: NCBI / ウイルスタイプ: VIRION / ウイルス・単離状態: STRAIN / ウイルス・エンベロープ: No / ウイルス・中空状態: Yes |
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宿主 | 生物種: ![]() |
分子量 | 理論値: 5 MDa |
ウイルス殻 | Shell ID: 1 / 直径: 300 Å / T番号(三角分割数): 4 |
-実験情報
-構造解析
手法 | ネガティブ染色法, クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.8 mg/mL |
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緩衝液 | pH: 7.6 / 詳細: 0.15 M phosphate buffered saline(PBS) buffer |
染色 | タイプ: NEGATIVE 詳細: Grids were plunge-frozen into liquid ethane using a FEI Mark IV virtobot, after 2s blotting to remove extra sample. |
グリッド | 詳細: 200 mesh R1.2x1.3 Quantifoil Cu grid, glow discharged in air |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 120 K / 装置: FEI VITROBOT MARK IV / 手法: Blot for 2 seconds before plunging |
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電子顕微鏡法
顕微鏡 | FEI TITAN |
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アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected at 75000 magnification |
日付 | 2014年10月9日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 実像数: 320 / 平均電子線量: 16 e/Å2 詳細: Every image is the average of seven frames recorded by the direct electron detector |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 0.005 mm / 最大 デフォーカス(公称値): 3.5 µm / 最小 デフォーカス(公称値): 2.0 µm / 倍率(公称値): 37000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
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画像解析
詳細 | The particles were boxed using e2boxer.py. CTF fitting was automatically performed using fitctf2.py in jspr, then visually validated and adjusted using EMAN1.9 ctfit program. The gold standard 3D reconstruction procedure was followed using jspr package, with the datasets split into two halves in the beginning. |
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CTF補正 | 詳細: Each particle |
最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 6.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: jspr, EMAN, EMAN2 / 使用した粒子像数: 1303 |