+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-6148 | |||||||||
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タイトル | Cryo-EM reconstruction of poliovirus-receptor complex | |||||||||
マップデータ | Reconstruction of receptor-decorated poliovirus at 0.4 nm resolution, sharpened with a B-factor of -60 | |||||||||
試料 |
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キーワード | poliovirus / receptor / PVR / CD155 | |||||||||
機能・相同性 | 機能・相同性情報 susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / adherens junction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...susceptibility to T cell mediated cytotoxicity / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / adherens junction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / virus receptor activity / focal adhesion / cell surface / extracellular space / membrane / plasma membrane / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Human poliovirus 1 Mahoney (ポリオウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.0 Å | |||||||||
データ登録者 | Strauss M / Filman DJ / Cheng N / Noel RT / Belnap DM / Hogle JM | |||||||||
引用 | ジャーナル: J Virol / 年: 2015 タイトル: Nectin-like interactions between poliovirus and its receptor trigger conformational changes associated with cell entry. 著者: Mike Strauss / David J Filman / David M Belnap / Naiqian Cheng / Roane T Noel / James M Hogle / 要旨: Poliovirus infection is initiated by attachment to a receptor on the cell surface called Pvr or CD155. At physiological temperatures, the receptor catalyzes an irreversible expansion of the virus to ...Poliovirus infection is initiated by attachment to a receptor on the cell surface called Pvr or CD155. At physiological temperatures, the receptor catalyzes an irreversible expansion of the virus to form an expanded form of the capsid called the 135S particle. This expansion results in the externalization of the myristoylated capsid protein VP4 and the N-terminal extension of the capsid protein VP1, both of which become inserted into the cell membrane. Structures of the expanded forms of poliovirus and of several related viruses have recently been reported. However, until now, it has been unclear how receptor binding triggers viral expansion at physiological temperature. Here, we report poliovirus in complex with an enzymatically partially deglycosylated form of the 3-domain ectodomain of Pvr at a 4-Å resolution, as determined by cryo-electron microscopy. The interaction of the receptor with the virus in this structure is reminiscent of the interactions of Pvr with its natural ligands. At a low temperature, the receptor induces very few changes in the structure of the virus, with the largest changes occurring within the footprint of the receptor, and in a loop of the internal protein VP4. Changes in the vicinity of the receptor include the displacement of a natural lipid ligand (called "pocket factor"), demonstrating that the loss of this ligand, alone, is not sufficient to induce particle expansion. Finally, analogies with naturally occurring ligand binding in the nectin family suggest which specific structural rearrangements in the virus-receptor complex could help to trigger the irreversible expansion of the capsid. IMPORTANCE: The cell-surface receptor (Pvr) catalyzes a large structural change in the virus that exposes membrane-binding protein chains. We fitted known atomic models of the virus and Pvr into ...IMPORTANCE: The cell-surface receptor (Pvr) catalyzes a large structural change in the virus that exposes membrane-binding protein chains. We fitted known atomic models of the virus and Pvr into three-dimensional experimental maps of the receptor-virus complex. The molecular interactions we see between poliovirus and its receptor are reminiscent of the nectin family, by involving the burying of otherwise-exposed hydrophobic groups. Importantly, poliovirus expansion is regulated by the binding of a lipid molecule within the viral capsid. We show that receptor binding either causes this molecule to be expelled or requires it, but that its loss is not sufficient to trigger irreversible expansion. Based on our model, we propose testable hypotheses to explain how the viral shell becomes destabilized, leading to RNA uncoating. These findings give us a better understanding of how poliovirus has evolved to exploit a natural process of its host to penetrate the membrane barrier. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_6148.map.gz | 829.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-6148-v30.xml emd-6148.xml | 13.6 KB 13.6 KB | 表示 表示 | EMDBヘッダ |
画像 | 400_6148.gif 80_6148.gif | 133.6 KB 6.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-6148 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6148 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_6148_validation.pdf.gz | 78.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_6148_full_validation.pdf.gz | 77.3 KB | 表示 | |
XML形式データ | emd_6148_validation.xml.gz | 493 B | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6148 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6148 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_6148.map.gz / 形式: CCP4 / 大きさ: 976.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of receptor-decorated poliovirus at 0.4 nm resolution, sharpened with a B-factor of -60 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.986 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
-試料の構成要素
-全体 : Type I poliovirus (Mahoney) in complex with enzymatically deglyco...
全体 | 名称: Type I poliovirus (Mahoney) in complex with enzymatically deglycosylated 3-ecto-domain receptor (PVR, CD155) |
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要素 |
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-超分子 #1000: Type I poliovirus (Mahoney) in complex with enzymatically deglyco...
超分子 | 名称: Type I poliovirus (Mahoney) in complex with enzymatically deglycosylated 3-ecto-domain receptor (PVR, CD155) タイプ: sample / ID: 1000 / 集合状態: 1 icosahedral virus + 60 receptors / Number unique components: 2 |
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分子量 | 理論値: 12 MDa |
-超分子 #1: Human poliovirus 1 Mahoney
超分子 | 名称: Human poliovirus 1 Mahoney / タイプ: virus / ID: 1 / NCBI-ID: 12081 / 生物種: Human poliovirus 1 Mahoney / Sci species strain: Mahoney / 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: No |
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宿主 | 生物種: Homo sapiens (ヒト) / 別称: VERTEBRATES |
分子量 | 理論値: 9 MDa |
ウイルス殻 | Shell ID: 1 / 直径: 165 Å / T番号(三角分割数): 1 |
-分子 #1: Poliovirus receptor
分子 | 名称: Poliovirus receptor / タイプ: protein_or_peptide / ID: 1 / Name.synonym: PVR/CD155, Nectin-like protein 5, NECL-5 / 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: Homo sapiens (ヒト) / 別称: human |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | UniProtKB: Poliovirus receptor |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 1.0 mg/mL |
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緩衝液 | pH: 7 / 詳細: PBS |
グリッド | 詳細: 200 mesh Cu grid with fenestrated carbon support |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 45 % / チャンバー内温度: 120 K / 装置: HOMEMADE PLUNGER / 手法: Sample mixed and frozen within 2 minutes. |
-電子顕微鏡法
顕微鏡 | FEI POLARA 300 |
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温度 | 最低: 80 K / 最高: 165 K / 平均: 100 K |
アライメント法 | Legacy - Electron beam tilt params: 0 |
詳細 | K2 Summit super-resolution mode used |
日付 | 2013年11月1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: 280 / 平均電子線量: 25 e/Å2 / 詳細: The last 22 frames of a 24-frame stack were used. / ビット/ピクセル: 8 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 25355 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.26 mm / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 27500 |
試料ステージ | 試料ホルダーモデル: OTHER |
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
-画像解析
CTF補正 | 詳細: per micrograph |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Relion1.2, GeFrealign / 詳細: This map has a B-factor of -60 applied to it. / 使用した粒子像数: 9248 |
-原子モデル構築 1
初期モデル | PDB ID: Chain - #0 - Chain ID: 1 / Chain - #1 - Chain ID: 2 / Chain - #2 - Chain ID: 3 / Chain - #3 - Chain ID: 4 |
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ソフトウェア | 名称: Coot, spdbv, Refmac5 |
詳細 | After rigid-body fitting, manual model building was alternated with automated stereochemically restrained refinement, minimizing the discrepancy between experimental and model-based Fourier amplitudes and phases. |
精密化 | 空間: RECIPROCAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: pseudo-real space |
-原子モデル構築 2
初期モデル | PDB ID: Chain - Chain ID: A |
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ソフトウェア | 名称: Coot, spdbv, Refmac5 |
詳細 | After rigid-body fitting, manual model building was alternated with automated stereochemically restrained refinement, minimizing the discrepancy between experimental and model-based Fourier amplitudes and phases. |
精密化 | 空間: RECIPROCAL / プロトコル: FLEXIBLE FIT / 当てはまり具合の基準: pseudo-real space |