+
データを開く
-
基本情報
| 登録情報 | データベース: PDB / ID: 8xko | |||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| タイトル | CryoEM structure of compound HNC-1664 bound with RdRP-RNA complex of SARS-CoV-2 | |||||||||||||||||||||||||||||||||||||||
要素 |
| |||||||||||||||||||||||||||||||||||||||
キーワード | VIRAL PROTEIN/RNA / RNA dependent RNA polymerase / SARS-CoV-2 / nucleoside analog / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex | |||||||||||||||||||||||||||||||||||||||
| 機能・相同性 | 機能・相同性情報protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 5'-3' RNA helicase activity / 付加脱離酵素(リアーゼ); P-Oリアーゼ類; - / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 5'-3' RNA helicase activity / 付加脱離酵素(リアーゼ); P-Oリアーゼ類; - / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / snRNP Assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エキソリボヌクレアーゼ / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host toll-like receptor signaling pathway / G-quadruplex RNA binding / mRNA guanylyltransferase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / DNA helicase / symbiont-mediated suppression of host NF-kappaB cascade / SARS-CoV-2 modulates host translation machinery / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell Golgi apparatus / methyltransferase cap1 activity / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ / lyase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding 類似検索 - 分子機能 | |||||||||||||||||||||||||||||||||||||||
| 生物種 | ![]() Severe acute respiratory syndrome coronavirus (SARS コロナウイルス)synthetic construct (人工物) | |||||||||||||||||||||||||||||||||||||||
| 手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.29 Å | |||||||||||||||||||||||||||||||||||||||
データ登録者 | Li, M. / An, L. / Hong, Y. / Li, S. / Zhang, K. | |||||||||||||||||||||||||||||||||||||||
| 資金援助 | 中国, 1件
| |||||||||||||||||||||||||||||||||||||||
引用 | ジャーナル: Nat Commun / 年: 2024タイトル: An adenosine analog shows high antiviral potency against coronavirus and arenavirus mainly through an unusual base pairing mode. 著者: Xiaoying Jia / Xuping Jing / Ming Li / Minli Gao / Yao Zhong / Entao Li / Yang Liu / Rui Li / Guoqiang Yao / Qiaojie Liu / Minmin Zhou / Yuxia Hou / Linfeng An / Yibao Hong / Shanshan Li / ...著者: Xiaoying Jia / Xuping Jing / Ming Li / Minli Gao / Yao Zhong / Entao Li / Yang Liu / Rui Li / Guoqiang Yao / Qiaojie Liu / Minmin Zhou / Yuxia Hou / Linfeng An / Yibao Hong / Shanshan Li / Jiancun Zhang / Wei Wang / Kaiming Zhang / Peng Gong / Sandra Chiu / ![]() 要旨: By targeting the essential viral RNA-dependent RNA polymerase (RdRP), nucleoside analogs (NAs) have exhibited great potential in antiviral therapy for RNA virus-related diseases. However, most ribose- ...By targeting the essential viral RNA-dependent RNA polymerase (RdRP), nucleoside analogs (NAs) have exhibited great potential in antiviral therapy for RNA virus-related diseases. However, most ribose-modified NAs do not present broad-spectrum features, likely due to differences in ribose-RdRP interactions across virus families. Here, we show that HNC-1664, an adenosine analog with modifications both in ribose and base, has broad-spectrum antiviral activity against positive-strand coronaviruses and negative-strand arenaviruses. Importantly, treatment with HNC-1664 demonstrate anti-SARS-CoV-2 efficacy in infected K18-human ACE2 mice, with reduced viral titer and mortality, as well as improved lung injury. Enzymology data demonstrate that HNC-1664 inhibits RNA synthesis mainly at the pre-catalysis stage. The cryo-EM structures of HNC-1664-bound RdRP-RNA complexes from both SARS-CoV-2 and LASV reveal an unusual base pairing mode of HNC-1664 in part due to its base modification, thus revealing its great potency in binding but not catalysis. Under certain circumstances, 1664-TP can be slowly incorporated by RdRP through regular Watson-Crick base pairing, as evidenced by enzymology data and an HNC-1664-incorporated crystal structure of the RdRP-RNA complex. Overall, HNC-1664 achieves broad-spectrum characteristics by favoring an alternative base pairing strategy to non-catalytically block RNA synthesis, providing a novel concept for the rational development of NA drugs. | |||||||||||||||||||||||||||||||||||||||
| 履歴 |
|
-
構造の表示
| 構造ビューア | 分子: Molmil Jmol/JSmol |
|---|
-
ダウンロードとリンク
-
ダウンロード
| PDBx/mmCIF形式 | 8xko.cif.gz | 255.2 KB | 表示 | PDBx/mmCIF形式 |
|---|---|---|---|---|
| PDB形式 | pdb8xko.ent.gz | 表示 | PDB形式 | |
| PDBx/mmJSON形式 | 8xko.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
| その他 | その他のダウンロード |
-検証レポート
| アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/xk/8xko ftp://data.pdbj.org/pub/pdb/validation_reports/xk/8xko | HTTPS FTP |
|---|
-関連構造データ
-
リンク
-
集合体
| 登録構造単位 | ![]()
|
|---|---|
| 1 |
|
-
要素
-タンパク質 , 1種, 1分子 A
| #1: タンパク質 | 分子量: 108350.703 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() 遺伝子: rep, 1a-1b / 発現宿主: ![]() 参照: UniProt: P0DTD1, RNA-directed RNA polymerase, mRNA guanylyltransferase |
|---|
-Non-structural protein ... , 2種, 3分子 BDC
| #2: タンパク質 | 分子量: 23455.707 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Severe acute respiratory syndrome coronavirus (SARS コロナウイルス)遺伝子: rep, 1a-1b / 発現宿主: ![]() #3: タンパク質 | | 分子量: 10077.685 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Severe acute respiratory syndrome coronavirus (SARS コロナウイルス)遺伝子: rep, 1a-1b / 発現宿主: ![]() |
|---|
-RNA鎖 , 2種, 2分子 EF
| #4: RNA鎖 | 分子量: 4462.708 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
|---|---|
| #5: RNA鎖 | 分子量: 5993.537 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
-非ポリマー , 2種, 4分子 
| #6: 化合物 | ChemComp-A1LVZ / [[( 分子量: 633.092 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C12H16FIN3O12P3 |
|---|---|
| #7: 化合物 |
-詳細
| 研究の焦点であるリガンドがあるか | Y |
|---|---|
| Has protein modification | N |
-実験情報
-実験
| 実験 | 手法: 電子顕微鏡法 |
|---|---|
| EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-
試料調製
| 構成要素 | 名称: CryoEM structure of compound HNC-1644 bound with RdRP-RNA タイプ: COMPLEX / Entity ID: #1-#5 / 由来: MULTIPLE SOURCES |
|---|---|
| 分子量 | 値: 0.15 MDa / 実験値: YES |
| 由来(天然) | 生物種: Severe acute respiratory syndrome coronavirus (SARS コロナウイルス) |
| 由来(組換発現) | 生物種: ![]() |
| 緩衝液 | pH: 7.5 |
| 試料 | 濃度: 5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
| 急速凍結 | 凍結剤: ETHANE |
-
電子顕微鏡撮影
| 実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
|---|---|
| 顕微鏡 | モデル: FEI TITAN KRIOS |
| 電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
| 電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3200 nm / 最小 デフォーカス(公称値): 1600 nm |
| 撮影 | 電子線照射量: 53.4 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-
解析
| EMソフトウェア |
| ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
| 粒子像の選択 | 選択した粒子像数: 1688273 | ||||||||||||||||||||||||
| 対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||
| 3次元再構成 | 解像度: 3.29 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 467095 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
| 拘束条件 |
|
ムービー
コントローラー
万見について






中国, 1件
引用



PDBj







































FIELD EMISSION GUN