+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3880 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1 | |||||||||
マップデータ | Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1 | |||||||||
試料 |
| |||||||||
機能・相同性 | 機能・相同性情報 regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / : / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / adhesion of symbiont to host / RNA-protein covalent cross-linking ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / : / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / adhesion of symbiont to host / RNA-protein covalent cross-linking / : / : / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / leukocyte migration / Interleukin-10 signaling / immunological synapse / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 / cellular response to leukemia inhibitory factor / cellular response to glucose stimulus / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / transmembrane signaling receptor activity / integrin binding / cellular response to amyloid-beta / symbiont-mediated suppression of host gene expression / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / viral capsid / virus receptor activity / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / signaling receptor activity / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / positive regulation of ERK1 and ERK2 cascade / RNA helicase activity / receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / cell adhesion / symbiont entry into host cell / membrane raft / induction by virus of host autophagy / external side of plasma membrane / 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 / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | Coxsackievirus A24 (コクサッキーウイルス) / homo sapiens (ヒト) / Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
データ登録者 | Hurdiss DL / Ranson NA | |||||||||
引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2018 タイトル: Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus. 著者: Jim Baggen / Daniel L Hurdiss / Georg Zocher / Nitesh Mistry / Richard W Roberts / Jasper J Slager / Hongbo Guo / Arno L W van Vliet / Maryam Wahedi / Kimberley Benschop / Erwin Duizer / ...著者: Jim Baggen / Daniel L Hurdiss / Georg Zocher / Nitesh Mistry / Richard W Roberts / Jasper J Slager / Hongbo Guo / Arno L W van Vliet / Maryam Wahedi / Kimberley Benschop / Erwin Duizer / Cornelis A M de Haan / Erik de Vries / José M Casasnovas / Raoul J de Groot / Niklas Arnberg / Thilo Stehle / Neil A Ranson / Hendrik Jan Thibaut / Frank J M van Kuppeveld / 要旨: Acute hemorrhagic conjunctivitis (AHC) is a painful, contagious eye disease, with millions of cases in the last decades. Coxsackievirus A24 (CV-A24) was not originally associated with human disease, ...Acute hemorrhagic conjunctivitis (AHC) is a painful, contagious eye disease, with millions of cases in the last decades. Coxsackievirus A24 (CV-A24) was not originally associated with human disease, but in 1970 a pathogenic "variant" (CV-A24v) emerged, which is now the main cause of AHC. Initially, this variant circulated only in Southeast Asia, but it later spread worldwide, accounting for numerous AHC outbreaks and two pandemics. While both CV-A24 variant and nonvariant strains still circulate in humans, only variant strains cause AHC for reasons that are yet unknown. Since receptors are important determinants of viral tropism, we set out to map the CV-A24 receptor repertoire and establish whether changes in receptor preference have led to the increased pathogenicity and rapid spread of CV-A24v. Here, we identify ICAM-1 as an essential receptor for both AHC-causing and non-AHC strains. We provide a high-resolution cryo-EM structure of a virus-ICAM-1 complex, which revealed critical ICAM-1-binding residues. These data could help identify a possible conserved mode of receptor engagement among ICAM-1-binding enteroviruses and rhinoviruses. Moreover, we identify a single capsid substitution that has been adopted by all pandemic CV-A24v strains and we reveal that this adaptation enhances the capacity of CV-A24v to bind sialic acid. Our data elucidate the CV-A24v receptor repertoire and point to a role of enhanced receptor engagement in the adaptation to the eye, possibly enabling pandemic spread. | |||||||||
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_3880.map.gz | 219.1 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-3880-v30.xml emd-3880.xml | 19 KB 19 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_3880_fsc.xml | 15.9 KB | 表示 | FSCデータファイル |
画像 | emd_3880.png | 237.8 KB | ||
その他 | emd_3880_additional.map.gz | 302.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3880 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3880 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_3880_validation.pdf.gz | 306.5 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_3880_full_validation.pdf.gz | 305.6 KB | 表示 | |
XML形式データ | emd_3880_validation.xml.gz | 14.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3880 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3880 | 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_3880.map.gz / 形式: CCP4 / 大きさ: 381.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.0651 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
-追加マップ: Coxsackievirus A24v in complex with the D1-D2 fragment...
ファイル | emd_3880_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1 (unsharpened map). | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
-全体 : Coxsackievirus A24v in complex with the D1 and D2 domains of ICAM-1
全体 | 名称: Coxsackievirus A24v in complex with the D1 and D2 domains of ICAM-1 |
---|---|
要素 |
|
-超分子 #1: Coxsackievirus A24v in complex with the D1 and D2 domains of ICAM-1
超分子 | 名称: Coxsackievirus A24v in complex with the D1 and D2 domains of ICAM-1 タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
---|---|
分子量 | 理論値: 8 MDa |
-超分子 #2: Coxsackievirus A24
超分子 | 名称: Coxsackievirus A24 / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1-#3 |
---|---|
由来(天然) | 生物種: Coxsackievirus A24 (コクサッキーウイルス) |
-超分子 #3: D1 and D2 domains of ICAM-1
超分子 | 名称: D1 and D2 domains of ICAM-1 / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #4 |
---|---|
由来(天然) | 生物種: homo sapiens (ヒト) |
組換発現 | 生物種: Cricetulus griseus (モンゴルキヌゲネズミ) |
-分子 #1: VP1
分子 | 名称: VP1 / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Coxsackievirus A24 (コクサッキーウイルス) |
分子量 | 理論値: 34.378371 KDa |
配列 | 文字列: GIEETIDTVI TNALQLSQPK PQKQPTAQST PLTSGVNSQE VPALTAVETG ASGQAVPSDV IETRHVVNYK TRSESTLESF FGRSACVTI LEVENFNATT DADRKKQFTT WAITYTDTVQ LRRKLEFFTY SRFDLEMTFV ITERYYASNT GHARNQVYQL M YIPPGAPR ...文字列: GIEETIDTVI TNALQLSQPK PQKQPTAQST PLTSGVNSQE VPALTAVETG ASGQAVPSDV IETRHVVNYK TRSESTLESF FGRSACVTI LEVENFNATT DADRKKQFTT WAITYTDTVQ LRRKLEFFTY SRFDLEMTFV ITERYYASNT GHARNQVYQL M YIPPGAPR PTAWDDYTWQ SSSNPSVFYT YGSAPPRMSI PYVGIANAYS HFYDGFARVP LKDETVDSGD TYYGLVTIND FG TLAVRVV NEYNPARITS KIRVYMKPKH VRCWCPRPPR AVPYRGEGVD FKQDSITPLT AVENINTF |
-分子 #2: VP2
分子 | 名称: VP2 / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Coxsackievirus A24 (コクサッキーウイルス) |
分子量 | 理論値: 29.817412 KDa |
配列 | 文字列: SPNVEACGYS DRVRQITLGN STITTQEAAN AVVAYGEWPS YLDDKEANPI DAPTEPDVSS NRFYTLDSVQ WKSTSRGWWW KLPDALKDM GMFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAIPE YVMACNTEAK TSYVSYVNAN PGEKGGVFDN A YNPSAEAS ...文字列: SPNVEACGYS DRVRQITLGN STITTQEAAN AVVAYGEWPS YLDDKEANPI DAPTEPDVSS NRFYTLDSVQ WKSTSRGWWW KLPDALKDM GMFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAIPE YVMACNTEAK TSYVSYVNAN PGEKGGVFDN A YNPSAEAS EGRKFAALDY LLGCGVLAGN AFVYPHQIIN LRTNNSATLV LPYVNSLAID CMAKHNNWGL VILPLCKLDY AP NSSTEIP ITVTIAPMFT EFNGLRNITV PATQ |
-分子 #3: VP3
分子 | 名称: VP3 / タイプ: protein_or_peptide / ID: 3 / コピー数: 1 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Coxsackievirus A24 (コクサッキーウイルス) |
分子量 | 理論値: 26.637746 KDa |
配列 | 文字列: GLPTMLTPGS SQFLTSDDFQ SPCALPNFDV TPPIHIPGEV FNMMELAEID SMIPMNSVTG KANTMEMYPI PLDDKGSATP IFSISLSPA SDKRLQYTML GEILNYYTHW TGSLRFTFLF CGSMMATGKI LLSYSPPGAK PPTTRKDAML GTHIIWDLGL Q SSCTMLAP ...文字列: GLPTMLTPGS SQFLTSDDFQ SPCALPNFDV TPPIHIPGEV FNMMELAEID SMIPMNSVTG KANTMEMYPI PLDDKGSATP IFSISLSPA SDKRLQYTML GEILNYYTHW TGSLRFTFLF CGSMMATGKI LLSYSPPGAK PPTTRKDAML GTHIIWDLGL Q SSCTMLAP WISNTVYRRC IKDDFTEGGY ITCFYQTRIV VPSGTPTSMF MLAFVSACPD FSVRLLRDTN HISQRTLFAR AQ |
-分子 #4: Intercellular adhesion molecule 1
分子 | 名称: Intercellular adhesion molecule 1 / タイプ: protein_or_peptide / ID: 4 / コピー数: 1 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 9.2976 KDa |
組換発現 | 生物種: Cricetulus griseus (モンゴルキヌゲネズミ) |
配列 | 文字列: QTSVSPSKVI LPRGGSVLVT CSTSCDQPKL LGIETPLPKK ELLLPGNNRK VYELSNVQED SQPMCYSNCP DGQSTAKTFL TVYWT |
-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
濃度 | 10 mg/mL |
---|---|
緩衝液 | pH: 7.5 詳細: TBS buffer (Coxsackievirus A24v) Phosphate buffer (ICAM-1 D1-D2) |
グリッド | モデル: Lacey grids coated in a 3 nm carbon film (Agar Scientific, UK) 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 3.0 nm / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 80 % / チャンバー内温度: 8 K / 装置: LEICA EM GP 詳細: On-grid binding of the receptor was performed by applying 3 microliters of ICAM-1 (9.85 mg/ml) to the pre-blotted, virus-containing grid, and leaving for 30 seconds before blotting and freezing. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 検出モード: INTEGRATING / 撮影したグリッド数: 1 / 実像数: 2652 / 平均露光時間: 1.5 sec. / 平均電子線量: 60.0 e/Å2 |
電子線 | 加速電圧: 300 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 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: OTHER |
---|---|
得られたモデル | PDB-6eit: |