+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-26072 | |||||||||
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タイトル | Coxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-1 | |||||||||
マップデータ | Coxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-1 - Main Map | |||||||||
試料 |
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キーワード | polyclonal antibodies (ポリクローナル抗体) / immune complex / cryoEM (低温電子顕微鏡法) / VIRUS-IMMUNE SYSTEM complex | |||||||||
機能・相同性 | 機能・相同性情報 ピコルナイン2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...ピコルナイン2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / RNA helicase activity / induction by virus of host autophagy / RNA依存性RNAポリメラーゼ / virus-mediated perturbation of host defense response / 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 / タンパク質分解 / RNA binding / ATP binding / metal ion binding 類似検索 - 分子機能 | |||||||||
生物種 | Coxsackievirus A21 (コクサッキーウイルス) / Mus musculus (ハツカネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.8 Å | |||||||||
データ登録者 | Antanasijevic A / Ward AB | |||||||||
資金援助 | 1件
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引用 | ジャーナル: PNAS Nexus / 年: 2022 タイトル: High-resolution structural analysis of enterovirus-reactive polyclonal antibodies in complex with whole virions. 著者: Aleksandar Antanasijevic / Autumn J Schulze / Vijay S Reddy / Andrew B Ward / 要旨: Non-polio enteroviruses (NPEVs) cause serious illnesses in young children and neonates, including aseptic meningitis, encephalitis, and inflammatory muscle disease, among others. While over 100 ...Non-polio enteroviruses (NPEVs) cause serious illnesses in young children and neonates, including aseptic meningitis, encephalitis, and inflammatory muscle disease, among others. While over 100 serotypes have been described to date, vaccine only exists for EV-A71. Efforts toward rationally designed pan-NPEV vaccines would greatly benefit from structural biology methods for rapid and comprehensive evaluation of vaccine candidates and elicited antibody responses. Toward this goal, we introduced a cryo-electron-microscopy-based approach for structural analysis of virus- or vaccine-elicited polyclonal antibodies (pAbs) in complex with whole NPEV virions. We demonstrated the feasibility using coxsackievirus A21 and reconstructed five structurally distinct pAbs bound to the virus. The pAbs targeted two immunodominant epitopes, one overlapping with the receptor binding site. These results demonstrate that our method can be applied to map broad-spectrum polyclonal immune responses against intact virions and define potentially cross-reactive epitopes. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_26072.map.gz | 78.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-26072-v30.xml emd-26072.xml | 26.5 KB 26.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_26072_fsc.xml | 10 KB | 表示 | FSCデータファイル |
画像 | emd_26072.png | 121.5 KB | ||
マスクデータ | emd_26072_msk_1.map | 83.7 MB | マスクマップ | |
Filedesc metadata | emd-26072.cif.gz | 6.9 KB | ||
その他 | emd_26072_half_map_1.map.gz emd_26072_half_map_2.map.gz | 65.4 MB 65.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-26072 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26072 | HTTPS FTP |
-関連構造データ
関連構造データ | 7tquMC 7tqsC 7tqtC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_26072.map.gz / 形式: CCP4 / 大きさ: 83.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Coxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-1 - Main Map | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.045 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | emd_26072_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Coxsackievirus A21 capsid subdomain in complex with mouse...
ファイル | emd_26072_half_map_1.map | ||||||||||||
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注釈 | Coxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-1 - Half-map 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Coxsackievirus A21 capsid subdomain in complex with mouse...
ファイル | emd_26072_half_map_2.map | ||||||||||||
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注釈 | Coxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-1 - Half-map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Immune complex featuring subdomains of coxsackievirus A21 (CV-A21...
全体 | 名称: Immune complex featuring subdomains of coxsackievirus A21 (CV-A21) viral particles in complex with mouse polyclonal antibodies |
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要素 |
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-超分子 #1: Immune complex featuring subdomains of coxsackievirus A21 (CV-A21...
超分子 | 名称: Immune complex featuring subdomains of coxsackievirus A21 (CV-A21) viral particles in complex with mouse polyclonal antibodies タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#6 詳細: The complexes were assembled by combining purified CV-A21 particles and polyclonal antibodies isolated from mice (as Fab fragments) |
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由来(天然) | 生物種: Coxsackievirus A21 (コクサッキーウイルス) |
-分子 #1: pAbC-1 heavy chain
分子 | 名称: pAbC-1 heavy chain / タイプ: protein_or_peptide / ID: 1 / 詳細: Heavy Chain of the polyclonal antibody pAbC-1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 9.549763 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-分子 #2: pAbC-1 light chain
分子 | 名称: pAbC-1 light chain / タイプ: protein_or_peptide / ID: 2 / 詳細: Light Chain of the polyclonal antibody pAbC-1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 8.698714 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-分子 #3: VP1
分子 | 名称: VP1 / タイプ: protein_or_peptide / ID: 3 / 詳細: VP1 protein of the coxsackievirus A21 capsid / コピー数: 3 / 光学異性体: LEVO / EC番号: ピコルナイン2A |
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由来(天然) | 生物種: Coxsackievirus A21 (コクサッキーウイルス) |
分子量 | 理論値: 33.234238 KDa |
配列 | 文字列: GIEDLIDTAI KNALRVSQPP STQSTEATSG VNSQEVPALT AVETGASGQA IPSDVVETRH VVNYKTRSES CLESFFGRAA CVTILSLTN SSKSGEEKKH FNIWNITYTD TVQLRRKLEF FTYSRFDLEM TFVFTENYPS TASGEVRNQV YQIMYIPPGA P RPSSWDDY ...文字列: GIEDLIDTAI KNALRVSQPP STQSTEATSG VNSQEVPALT AVETGASGQA IPSDVVETRH VVNYKTRSES CLESFFGRAA CVTILSLTN SSKSGEEKKH FNIWNITYTD TVQLRRKLEF FTYSRFDLEM TFVFTENYPS TASGEVRNQV YQIMYIPPGA P RPSSWDDY TWQSSSNPSI FYMYGNAPPR MSIPYVGIAN AYSHFYDGFA RVPLEGENTD AGDTFYGLVS INDFGVLAVR AV NRSNPHT IHTSVRVYMK PKHIRCWCPR PPRAVLYRGE GVDMISSAIL PLAKVDSITT F UniProtKB: Genome polyprotein |
-分子 #4: VP2
分子 | 名称: VP2 / タイプ: protein_or_peptide / ID: 4 / 詳細: VP2 protein of the coxsackievirus A21 capsid / コピー数: 3 / 光学異性体: LEVO / EC番号: ピコルナイン2A |
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由来(天然) | 生物種: Coxsackievirus A21 (コクサッキーウイルス) |
分子量 | 理論値: 29.918537 KDa |
配列 | 文字列: SPNVEACGYS DRVRQITLGN STITTQEAAN AIVAYGEWPT YINDSEANPV DAPTEPDVSS NRFYTLESVS WKTTSRGWWW KLPDCLKDM GMFGQNMYYH YLGRSGYTIH VQCNASKFHQ GALGVFLIPE FVMACNTESK TSYVSYINAN PGERGGEFTN T YNPSNTDA ...文字列: SPNVEACGYS DRVRQITLGN STITTQEAAN AIVAYGEWPT YINDSEANPV DAPTEPDVSS NRFYTLESVS WKTTSRGWWW KLPDCLKDM GMFGQNMYYH YLGRSGYTIH VQCNASKFHQ GALGVFLIPE FVMACNTESK TSYVSYINAN PGERGGEFTN T YNPSNTDA SEGRKFAALD YLLGSGVLAG NAFVYPHQII NLRTNNSATI VVPYVNSLVI DCMAKHNNWG IVILPLAPLA FA ATSSPQV PITVTIAPMC TEFNGLRNIT VPVHQ UniProtKB: Genome polyprotein |
-分子 #5: VP3
分子 | 名称: VP3 / タイプ: protein_or_peptide / ID: 5 / 詳細: VP3 protein of the coxsackievirus A21 capsid / コピー数: 3 / 光学異性体: LEVO / EC番号: ピコルナイン2A |
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由来(天然) | 生物種: Coxsackievirus A21 (コクサッキーウイルス) |
分子量 | 理論値: 26.596703 KDa |
配列 | 文字列: GLPTMNTPGS NQFLTSDDFQ SPCALPNFDV TPPIHIPGEV KNMMELAEID TLIPMNAVDG KVNTMEMYQI PLNDNLSKAP IFCLSLSPA SDKRLSHTML GEILNYYTHW TGSIRFTFLF CGSMMATGKL LLSYSPPGAK PPTNRKDAML GTHIIWDLGL Q SSCSMVAP ...文字列: GLPTMNTPGS NQFLTSDDFQ SPCALPNFDV TPPIHIPGEV KNMMELAEID TLIPMNAVDG KVNTMEMYQI PLNDNLSKAP IFCLSLSPA SDKRLSHTML GEILNYYTHW TGSIRFTFLF CGSMMATGKL LLSYSPPGAK PPTNRKDAML GTHIIWDLGL Q SSCSMVAP WISNTVYRRC ARDDFTEGGF ITCFYQTRIV VPASTPTSMF MLGFVSACPD FSVRLLRDTP HISQSKLIGR TQ UniProtKB: Genome polyprotein |
-分子 #6: VP4
分子 | 名称: VP4 / タイプ: protein_or_peptide / ID: 6 / 詳細: VP4 protein of the coxsackievirus A21 capsid / コピー数: 3 / 光学異性体: LEVO / EC番号: ピコルナイン2A |
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由来(天然) | 生物種: Coxsackievirus A21 (コクサッキーウイルス) |
分子量 | 理論値: 7.442118 KDa |
配列 | 文字列: MGAQVSTQKT GAHENQNVAA NGSTINYTTI NYYKDSASNS ATRQDLSQDP SKFTEPVKDL MLKTAPALN UniProtKB: Genome polyprotein |
-分子 #7: MYRISTIC ACID
分子 | 名称: MYRISTIC ACID / タイプ: ligand / ID: 7 / コピー数: 3 / 式: MYR |
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分子量 | 理論値: 228.371 Da |
Chemical component information | ChemComp-MYR: |
-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 | 2.5 mg/mL | |||||||||
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緩衝液 | pH: 7.4 構成要素:
詳細: TBS, 0.2um filtered | |||||||||
グリッド | モデル: Quantifoil R2/1 / 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: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. | |||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 10 % / チャンバー内温度: 283 K / 装置: FEI VITROBOT MARK IV / 詳細: 3-7s blot time. | |||||||||
詳細 | The complex was generated by incubation of mouse polyclonal antibodies with recombinantly expressed CV-A21 virions and subsequent SEC purification. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 最大 デフォーカス(公称値): 1.8 µm / 最小 デフォーカス(公称値): 0.8 µm / 倍率(公称値): 130000 |
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 |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 撮影したグリッド数: 2 / 実像数: 3862 / 平均露光時間: 9.0 sec. / 平均電子線量: 50.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |