+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-6243 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Poliovirus complexed with soluble, deglycosylated poliovirus receptor (Pvr) at 4 degrees C | |||||||||
マップデータ | 3D reconstruction of poliovirus-receptor complex | |||||||||
試料 |
| |||||||||
キーワード | cell entry / enterovirus / glycosylation / icosahedral virus / icosahedron / picornavirus / virus entry / virus-receptor complex / virus-receptor interaction | |||||||||
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 / symbiont-mediated suppression of host translation initiation / 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 / 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 ...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 / symbiont-mediated suppression of host translation initiation / 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 / 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 / cell adhesion molecule binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS 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 / adherens junction / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / virus receptor activity / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / signaling receptor activity / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / focal adhesion / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / proteolysis / RNA binding / extracellular space / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Human poliovirus 1 (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: 9.0 Å | |||||||||
データ登録者 | Strauss M / Filman DJ / Belnap DM / Cheng N / Noel RT / 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 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_6243.map.gz | 43.4 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-6243-v30.xml emd-6243.xml | 9 KB 9 KB | 表示 表示 | EMDBヘッダ |
画像 | 400_6243.gif 80_6243.gif | 94.1 KB 6.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-6243 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6243 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_6243_validation.pdf.gz | 365.2 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_6243_full_validation.pdf.gz | 364.7 KB | 表示 | |
XML形式データ | emd_6243_validation.xml.gz | 7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6243 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6243 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_6243.map.gz / 形式: CCP4 / 大きさ: 88.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | 3D reconstruction of poliovirus-receptor complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.77182 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
-全体 : Poliovirus type 1 (Mahoney strain) bound to soluble, deglycosylat...
全体 | 名称: Poliovirus type 1 (Mahoney strain) bound to soluble, deglycosylated poliovirus receptor (Pvr) |
---|---|
要素 |
|
-超分子 #1000: Poliovirus type 1 (Mahoney strain) bound to soluble, deglycosylat...
超分子 | 名称: Poliovirus type 1 (Mahoney strain) bound to soluble, deglycosylated poliovirus receptor (Pvr) タイプ: sample / ID: 1000 / 集合状態: 60 Pvr bind to one poliovirus / Number unique components: 2 |
---|
-超分子 #1: Human poliovirus 1
超分子 | 名称: Human poliovirus 1 / タイプ: virus / ID: 1 / Name.synonym: poliovirus / NCBI-ID: 12080 / 生物種: Human poliovirus 1 / 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 / Syn species name: poliovirus |
---|---|
宿主 | 生物種: Homo sapiens (ヒト) / 別称: VERTEBRATES |
ウイルス殻 | Shell ID: 1 / 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, Nectin-like protein 5 / 組換発現: No / データベース: NCBI |
---|---|
由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: human |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
凍結 | 凍結剤: ETHANE / 装置: OTHER |
---|
-電子顕微鏡法
顕微鏡 | FEI/PHILIPS CM200FEG |
---|---|
日付 | 1999年11月1日 |
撮影 | カテゴリ: FILM / フィルム・検出器のモデル: KODAK SO-163 FILM / デジタル化 - スキャナー: ZEISS SCAI |
電子線 | 加速電圧: 120 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2 mm |
試料ステージ | 試料ホルダーモデル: GATAN LIQUID NITROGEN |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 9.0 Å / 解像度の算出法: OTHER / 使用した粒子像数: 3822 |
---|