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基本情報
登録情報 | データベース: EMDB / ID: EMD-6435 | |||||||||
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タイトル | VHH complexes with poliovirus: cryo-electron microscopy studies at near-atomic resolution | |||||||||
![]() | Reconstruction of VHH-poliovirus (PVSS21E - Mahoney Type 1) | |||||||||
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機能・相同性 | ![]() symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() ![]() | |||||||||
手法 | ![]() ![]() | |||||||||
![]() | Strauss M / Schotte L / Thys B / Filman DJ / Hogle JM | |||||||||
![]() | ![]() タイトル: Five of Five VHHs Neutralizing Poliovirus Bind the Receptor-Binding Site. 著者: Mike Strauss / Lise Schotte / Bert Thys / David J Filman / James M Hogle / ![]() ![]() 要旨: Nanobodies, or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In ...Nanobodies, or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In this study, we present high-resolution cryo-electron microscopy reconstructions of poliovirus with five neutralizing VHHs. All VHHs bind the capsid in the canyon at sites that extensively overlap the poliovirus receptor-binding site. In contrast, the interaction involves a unique (and surprisingly extensive) surface for each of the five VHHs. Five regions of the capsid were found to participate in binding with all five VHHs. Four of these five regions are known to alter during the expansion of the capsid associated with viral entry. Interestingly, binding of one of the VHHs, PVSS21E, resulted in significant changes of the capsid structure and thus seems to trap the virus in an early stage of expansion. IMPORTANCE: We describe the cryo-electron microscopy structures of complexes of five neutralizing VHHs with the Mahoney strain of type 1 poliovirus at resolutions ranging from 3.8 to 6.3Å. All five ...IMPORTANCE: We describe the cryo-electron microscopy structures of complexes of five neutralizing VHHs with the Mahoney strain of type 1 poliovirus at resolutions ranging from 3.8 to 6.3Å. All five VHHs bind deep in the virus canyon at similar sites that overlap extensively with the binding site for the receptor (CD155). The binding surfaces on the VHHs are surprisingly extensive, but despite the use of similar binding surfaces on the virus, the binding surface on the VHHs is unique for each VHH. In four of the five complexes, the virus remains essentially unchanged, but for the fifth there are significant changes reminiscent of but smaller in magnitude than the changes associated with cell entry, suggesting that this VHH traps the virus in a previously undescribed early intermediate state. The neutralizing mechanisms of the VHHs and their potential use as quality control agents for the end game of poliovirus eradication are discussed. | |||||||||
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構造の表示
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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 | ![]() | 418.9 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 13.1 KB 13.1 KB | 表示 表示 | ![]() |
画像 | ![]() ![]() | 120.8 KB 6.2 KB | ||
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-関連構造データ
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「今月の分子」の関連する項目 |
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マップ
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注釈 | Reconstruction of VHH-poliovirus (PVSS21E - Mahoney Type 1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.985 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 : Nanobody PVSS21E in complex with poliovirus P1/Mahoney
全体 | 名称: Nanobody PVSS21E in complex with poliovirus P1/Mahoney |
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要素 |
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-超分子 #1000: Nanobody PVSS21E in complex with poliovirus P1/Mahoney
超分子 | 名称: Nanobody PVSS21E in complex with poliovirus P1/Mahoney タイプ: sample / ID: 1000 / 詳細: 1 集合状態: 60 nanobody VHH monomers bind to each poliovirion Number unique components: 2 |
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分子量 | 実験値: 9.0 MDa / 理論値: 9.0 MDa / 手法: 1 |
-超分子 #1: Human poliovirus 1
超分子 | 名称: Human poliovirus 1 / タイプ: virus / ID: 1 / Name.synonym: poliovirus 詳細: The viral capsid is decorated with 60 copies of a single-domain antibody (PVSS21E). NCBI-ID: 12080 / 生物種: Human poliovirus 1 / データベース: NCBI / ウイルスタイプ: VIRION / ウイルス・単離状態: SEROTYPE / ウイルス・エンベロープ: No / ウイルス・中空状態: No / Syn species name: poliovirus / Sci species serotype: 1 |
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宿主 | 生物種: ![]() ![]() |
分子量 | 実験値: 7 MDa / 理論値: 7 MDa |
ウイルス殻 | Shell ID: 1 / 直径: 350 Å / T番号(三角分割数): 3 |
-分子 #1: PVSS21E
分子 | 名称: PVSS21E / タイプ: protein_or_peptide / ID: 1 / Name.synonym: nanobody, VHH 詳細: 60 copies of this single-domain antibody are attached to the viral capsid. コピー数: 60 / 集合状態: monomer / 組換発現: Yes |
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由来(天然) | 生物種: ![]() ![]() ![]() |
分子量 | 実験値: 15 KDa / 理論値: 15 KDa |
組換発現 | 生物種: ![]() ![]() ![]() |
-実験情報
-構造解析
手法 | ![]() |
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試料の集合状態 | particle |
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試料調製
濃度 | 1 mg/mL |
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緩衝液 | pH: 7.4 / 詳細: 145 mM NaCl, 50 mM Na2HPO4.12H2O |
グリッド | 詳細: C-flat 1.2/1.3 |
凍結 | 凍結剤: ETHANE / チャンバー内温度: 154 K / 装置: HOMEMADE PLUNGER / 手法: 4 second blot |
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電子顕微鏡法
顕微鏡 | FEI POLARA 300 |
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電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 25380.7 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD![]() |
試料ステージ | 試料ホルダー: Polara holder / 試料ホルダーモデル: OTHER |
温度 | 最低: 80 K / 最高: 110 K / 平均: 80 K |
アライメント法 | Legacy - Electron beam tilt params: 0 |
詳細 | Gatan K2 operated in Super-resolution mode |
日付 | 2013年11月27日 |
撮影 | カテゴリ: CCD / フィルム・検出器のモデル: GATAN K2 (4k x 4k) / デジタル化 - サンプリング間隔: 2.5 µm / 実像数: 300 / 平均電子線量: 25 e/Å2 / ビット/ピクセル: 8 |
実験機器 | ![]() モデル: Tecnai Polara / 画像提供: FEI Company |
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画像解析
CTF補正 | 詳細: per particle |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.8 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Frealign / 使用した粒子像数: 24717 |
詳細 | The particles were processed using Frealign. |
-原子モデル構築 1
初期モデル | PDB ID: |
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ソフトウェア | 名称: COOT, SPDBV, REFMAC5 |
詳細 | Using stereochemically and icosahedrally restrained maximum likelihood refinement in REFMAC5, a representative subset of the full atomic model with all neighbors present was built and refined to fit the corresponding subset of the experimental map. Portions of the model whose density resembled a structural homolog were identified and restrained to agree with the homolog. Detailed atomic models were constructed in areas of difference wherever the resolution of the map permitted. The Fourier-amplitude-weighted average cosine of the phase discrepancy was tracked. |
精密化 | 空間: RECIPROCAL / プロトコル: FLEXIBLE FIT 当てはまり具合の基準: ML agreement with Fourier amplitudes and phases |
得られたモデル | ![]() PDB-3jbg: |